4-167510453-T-C

Variant names:

• chr4-167510453-T-C
• rs10517942

Variant summary

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

The variant allele was found at a frequency of 0.356 in 151,864 control chromosomes in the GnomAD database, including 9,918 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 0.36 (9918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54084 AN: 151744 Hom.: 9919 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.356 AC: 54116 AN: 151864 Hom.: 9918 Cov.: 31 AF XY: 0.362 AC XY: 26833 AN XY: 74212

African (AFR) AF: 0.289 AC: 11953 AN: 41406

American (AMR) AF: 0.391 AC: 5971 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2545 AN: 5150

South Asian (SAS) AF: 0.400 AC: 1922 AN: 4806

European-Finnish (FIN) AF: 0.400 AC: 4215 AN: 10540

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24694 AN: 67912

Other (OTH) AF: 0.387 AC: 817 AN: 2110

Alfa AF: 0.369 Hom.: 26806

Bravo AF: 0.355

Asia WGS AF: 0.438 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10517942; hg19: chr4-168431604;