chr10-13278305-A-AGAT

Position:

chr10-13278305-A-AGAT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBP6BS2

The NM_006214.4(PHYH):c.1012_1013insATC(p.Asn337_Leu338insHis) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.00213 in 1,609,052 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L338L) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0022 ( 5 hom. )

Consequence

PHYH
NM_006214.4 inframe_insertion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:2B:2

Conservation

PhyloP100: 4.23

Variant links:

Genes affected

PHYH (HGNC:8940): (phytanoyl-CoA 2-hydroxylase) This gene is a member of the PhyH family and encodes a peroxisomal protein that is involved in the alpha-oxidation of 3-methyl branched fatty acids. Specifically, this protein converts phytanoyl-CoA to 2-hydroxyphytanoyl-CoA. Mutations in this gene have been associated with Refsum disease (RD) and deficient protein activity has been associated with Zellweger syndrome and rhizomelic chondrodysplasia punctata. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

PHYH links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_006214.4. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 10-13278305-A-AGAT is Benign according to our data. Variant chr10-13278305-A-AGAT is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 444210.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=2}.

BS2

High Homozygotes in GnomAdExome4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHYH	NM_006214.4 linkuse as main transcript	c.1012_1013insATC	p.Asn337_Leu338insHis	inframe_insertion	9/9	ENST00000263038.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHYH	ENST00000263038.9 linkuse as main transcript	c.1012_1013insATC	p.Asn337_Leu338insHis	inframe_insertion	9/9	1	NM_006214.4	P1	O14832-1
PHYH	ENST00000396913.6 linkuse as main transcript	c.712_713insATC	p.Asn237_Leu238insHis	inframe_insertion	8/8	5			O14832-2
PHYH	ENST00000396920.7 linkuse as main transcript	c.961_962insATC	p.Asn320_Leu321insHis	inframe_insertion	9/9	5

Frequencies

GnomAD3 genomes

AF:

0.00160

AC:

243

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00245

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00219

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00204

AC:

513

AN:

251408

Hom.:

AF XY:

0.00205

AC XY:

279

AN XY:

135890

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.00202

Gnomad ASJ exome

AF:

0.00109

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.00273

Gnomad NFE exome

AF:

0.00295

Gnomad OTH exome

AF:

0.00375

GnomAD4 exome

AF:

0.00218

AC:

3182

AN:

1456730

Hom.:

Cov.:

AF XY:

0.00209

AC XY:

1513

AN XY:

725128

show subpopulations

Gnomad4 AFR exome

AF:

0.000329

Gnomad4 AMR exome

AF:

0.00201

Gnomad4 ASJ exome

AF:

0.00149

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000162

Gnomad4 FIN exome

AF:

0.00283

Gnomad4 NFE exome

AF:

0.00247

Gnomad4 OTH exome

AF:

0.00226

GnomAD4 genome

AF:

0.00160

AC:

243

AN:

152322

Hom.:

Cov.:

AF XY:

0.00161

AC XY:

120

AN XY:

74486

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.00202

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00245

Gnomad4 NFE

AF:

0.00219

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00205

Hom.:

Bravo

AF:

0.00187

EpiCase

AF:

0.00196

EpiControl

AF:

0.00296

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:2Benign:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2023	PHYH: BS2 -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jan 07, 2022	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Nonsyndromic cleft lip palate

Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

University of Washington Center for Mendelian Genomics, University of Washington

Mar 27, 2016

- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 01, 2024

Variant summary: PHYH c.1010_1012dupATC (p.Asn337_Leu338insHis) results in an in-frame insertion that is predicted to insert 1 amino acid into the encoded protein. The variant allele was found at a frequency of 0.002 in 251408 control chromosomes in the gnomAD database, including 1 homozygote. c.1010_1012dupATC has been reported in the literature in individuals affected with retinal disease or nonsyndromic cleft lip and palate without strong evidence of causality (Watson_2014, Aylward_2016, Dieriro_2020). These reports do not provide unequivocal conclusions about association of the variant with Phytanic Acid Storage Disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25133751, 27229527, 32483926). ClinVar contains an entry for this variant (Variation ID: 444210). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over