rs7925536

Variant names:

• chr11-13178107-G-A
• rs7925536

Your query was ambiguous. Multiple possible variants found:

• chr11-13178107-G-A
• chr11-13178107-G-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 0.388 in 152,084 control chromosomes in the GnomAD database, including 12,998 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 0.39 (12998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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: 0.388 AC: 59027 AN: 151964 Hom.: 12996 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.388 AC: 59042 AN: 152084 Hom.: 12998 Cov.: 33 AF XY: 0.386 AC XY: 28721 AN XY: 74346

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.428

Alfa AF: 0.450 Hom.: 9983

Bravo AF: 0.377

Asia WGS AF: 0.277 AC: 965 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.032
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7925536; hg19: chr11-13199654;