rs7925640

Variant names:

• chr11-98665928-A-G
• rs7925640

Your query was ambiguous. Multiple possible variants found:

• chr11-98665928-A-G
• chr11-98665928-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 0.171 in 152,154 control chromosomes in the GnomAD database, including 2,311 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 0.17 (2311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25992 AN: 152038 Hom.: 2313 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.171 AC: 25994 AN: 152154 Hom.: 2311 Cov.: 32 AF XY: 0.170 AC XY: 12662 AN XY: 74374

African (AFR) AF: 0.221 AC: 9186 AN: 41494

American (AMR) AF: 0.124 AC: 1901 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3468

East Asian (EAS) AF: 0.122 AC: 629 AN: 5168

South Asian (SAS) AF: 0.191 AC: 922 AN: 4826

European-Finnish (FIN) AF: 0.161 AC: 1705 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10849 AN: 67990

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.165 Hom.: 5806

Bravo AF: 0.171

Asia WGS AF: 0.156 AC: 537 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.4
DANN	Benign	0.64
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7925640; hg19: chr11-98536658;