rs10014562

chr4-167698129-G-Achr4-167698129-G-Cchr4-167698129-G-T

Variant summary

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

The variant allele was found at a frequency of 0.641 in 151,874 control chromosomes in the GnomAD database, including 32,394 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 0.64 (32394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97353 AN: 151756 Hom.: 32396 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.658

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.641 AC: 97389 AN: 151874 Hom.: 32394 Cov.: 32 AF XY: 0.650 AC XY: 48239 AN XY: 74240

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.655

Alfa AF: 0.632 Hom.: 3569

Bravo AF: 0.635

Asia WGS AF: 0.797 AC: 2769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.31
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10014562; hg19: chr4-168619280; COSMIC: COSV66847393;