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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.171 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

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.154

Alfa AF: 0.161 Hom.: 3208

Bravo AF: 0.171

Asia WGS AF: 0.156 AC: 537 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7925640; hg19: chr11-98536658;