rs10517938

Variant names:

• chr4-167433268-A-C
• rs10517938

Your query was ambiguous. Multiple possible variants found:

• chr4-167433268-A-C
• chr4-167433268-A-G

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 0.222 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.207

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517938; hg19: chr4-168354419;