chr6-169708593-T-C

Variant names:

• chr6-169708593-T-C
• rs9371126
• ENST00000480008.1:n.2720A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000480008.1(PHF10):​n.2720A>G variant causes a non coding transcript exon 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 ENST00000480008.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHF10	NM_018288.4	c.1113+1643A>G		intron_variant	Intron 9 of 11	ENST00000339209.9	NP_060758.2
PHF10	NM_133325.3	c.1107+1643A>G		intron_variant	Intron 9 of 11		NP_579866.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF10	ENST00000339209.9	c.1113+1643A>G		intron_variant	Intron 9 of 11	1	NM_018288.4	ENSP00000341805.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.181 AC: 7508 AN: 41520

American (AMR) AF: 0.347 AC: 5304 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.637 AC: 3292 AN: 5168

South Asian (SAS) AF: 0.225 AC: 1084 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1988 AN: 10558

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10846 AN: 67978

Other (OTH) AF: 0.203 AC: 428 AN: 2110

Alfa AF: 0.174 Hom.: 315

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
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9371126; hg19: chr6-170108689;