4-167433268-A-C

Variant names:

• chr4-167433268-A-C
• rs10517938

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 0.222 in 152,116 control chromosomes in the GnomAD database, including 4,366 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 0.22 (4366 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33685 AN: 151998 Hom.: 4365 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.222 AC: 33704 AN: 152116 Hom.: 4366 Cov.: 33 AF XY: 0.228 AC XY: 16964 AN XY: 74338

African (AFR) AF: 0.132 AC: 5487 AN: 41528

American (AMR) AF: 0.239 AC: 3652 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2611 AN: 5148

South Asian (SAS) AF: 0.344 AC: 1655 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3051 AN: 10572

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15886 AN: 67988

Other (OTH) AF: 0.207 AC: 438 AN: 2112

Alfa AF: 0.219 Hom.: 736

Bravo AF: 0.212

Asia WGS AF: 0.395 AC: 1367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10517938; hg19: chr4-168354419;