rs11923600

Variant names:

• chr3-176209663-G-A
• rs11923600

Your query was ambiguous. Multiple possible variants found:

• chr3-176209663-G-A
• chr3-176209663-G-T

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 0.163 in 152,058 control chromosomes in the GnomAD database, including 2,160 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 0.16 (2160 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.163 AC: 24792 AN: 151940 Hom.: 2158 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.163 AC: 24828 AN: 152058 Hom.: 2160 Cov.: 33 AF XY: 0.163 AC XY: 12079 AN XY: 74320

African (AFR) AF: 0.201 AC: 8329 AN: 41450

American (AMR) AF: 0.176 AC: 2684 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1537 AN: 5178

South Asian (SAS) AF: 0.101 AC: 488 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1222 AN: 10568

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9680 AN: 67982

Other (OTH) AF: 0.152 AC: 322 AN: 2112

Alfa AF: 0.147 Hom.: 4433

Bravo AF: 0.169

Asia WGS AF: 0.221 AC: 767 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.17
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11923600; hg19: chr3-175927451;