rs11974269

Variant names:

• chr7-21108059-A-C
• rs11974269

Your query was ambiguous. Multiple possible variants found:

• chr7-21108059-A-C
• chr7-21108059-A-G
• chr7-21108059-A-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 0.178 in 152,068 control chromosomes in the GnomAD database, including 2,645 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 0.18 (2645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 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: 0.178 AC: 27043 AN: 151950 Hom.: 2642 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.0773

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.178 AC: 27076 AN: 152068 Hom.: 2645 Cov.: 32 AF XY: 0.175 AC XY: 12987 AN XY: 74322

African (AFR) AF: 0.256 AC: 10590 AN: 41432

American (AMR) AF: 0.144 AC: 2203 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 644 AN: 3470

East Asian (EAS) AF: 0.179 AC: 925 AN: 5178

South Asian (SAS) AF: 0.258 AC: 1241 AN: 4810

European-Finnish (FIN) AF: 0.0773 AC: 819 AN: 10600

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10146 AN: 67988

Other (OTH) AF: 0.181 AC: 382 AN: 2112

Alfa AF: 0.160 Hom.: 8968

Bravo AF: 0.186

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs11974269; hg19: chr7-21147678; COSMIC: COSV57610662;