rs11927173

Variant names:

• chr3-23183703-T-C
• rs11927173

Your query was ambiguous. Multiple possible variants found:

• chr3-23183703-T-C
• chr3-23183703-T-G

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 0.126 in 152,144 control chromosomes in the GnomAD database, including 1,515 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 0.13 (1515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.126 AC: 19145 AN: 152026 Hom.: 1515 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0776

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.126 AC: 19154 AN: 152144 Hom.: 1515 Cov.: 32 AF XY: 0.131 AC XY: 9714 AN XY: 74368

African (AFR) AF: 0.200 AC: 8294 AN: 41498

American (AMR) AF: 0.0683 AC: 1045 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3470

East Asian (EAS) AF: 0.192 AC: 996 AN: 5180

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4822

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10570

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0776 AC: 5278 AN: 67990

Other (OTH) AF: 0.108 AC: 229 AN: 2116

Alfa AF: 0.101 Hom.: 157

Bravo AF: 0.118

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.81
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11927173; hg19: chr3-23225194;