rs11929140

Variant names:

• chr3-172437647-A-G
• rs11929140

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 0.141 in 152,218 control chromosomes in the GnomAD database, including 1,930 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 0.14 (1930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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: 0.141 AC: 21492 AN: 152100 Hom.: 1929 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.141 AC: 21506 AN: 152218 Hom.: 1930 Cov.: 32 AF XY: 0.151 AC XY: 11264 AN XY: 74432

African (AFR) AF: 0.130 AC: 5396 AN: 41548

American (AMR) AF: 0.145 AC: 2215 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1891 AN: 5180

South Asian (SAS) AF: 0.354 AC: 1702 AN: 4812

European-Finnish (FIN) AF: 0.228 AC: 2418 AN: 10588

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7143 AN: 68004

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.118 Hom.: 449

Bravo AF: 0.128

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.26
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11929140; hg19: chr3-172155437;