rs9371126

Positions:

• chr6-169708593-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612128.1(PHF10):​c.*1622A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,096 control chromosomes in the GnomAD database, including 4,113 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.21 (4113 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: PHF10 ENST00000612128.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521

Genes affected

PHF10 (HGNC:18250): (PHD finger protein 10) This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known. Sequence analysis suggests that multiple alternatively spliced transcript variants are derived from this gene but the full-length nature of only two of them is known. These two splice variants encode different isoforms. A pseudogene for this gene is located on Xq28. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF10	NM_018288.4	c.1113+1643A>G		intron_variant		ENST00000339209.9
PHF10	NM_133325.3	c.1107+1643A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF10	ENST00000339209.9	c.1113+1643A>G		intron_variant		1	NM_018288.4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31261 AN: 151978 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.205

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.206 AC: 31285 AN: 152096 Hom.: 4113 Cov.: 32 AF XY: 0.213 AC XY: 15822 AN XY: 74318

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.203

Alfa AF: 0.174 Hom.: 307

Bravo AF: 0.219

Asia WGS AF: 0.385 AC: 1333 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.1
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9371126; hg19: chr6-170108689;