rs4791943

Variant names:

• chr17-10212630-A-G
• rs4791943

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 0.105 in 152,172 control chromosomes in the GnomAD database, including 921 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 0.11 (921 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 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: 0.105 AC: 16023 AN: 152054 Hom.: 916 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.105 AC: 16052 AN: 152172 Hom.: 921 Cov.: 31 AF XY: 0.104 AC XY: 7705 AN XY: 74418

African (AFR) AF: 0.126 AC: 5232 AN: 41516

American (AMR) AF: 0.0957 AC: 1460 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0304 AC: 147 AN: 4828

European-Finnish (FIN) AF: 0.112 AC: 1191 AN: 10600

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7377 AN: 68002

Other (OTH) AF: 0.121 AC: 256 AN: 2110

Alfa AF: 0.105 Hom.: 544

Bravo AF: 0.107

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.76
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4791943; hg19: chr17-10115947;