rs7932964

Variant names:

• chr11-2049340-C-T
• rs7932964

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 0.324 in 151,736 control chromosomes in the GnomAD database, including 8,148 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 0.32 (8148 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 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: 0.324 AC: 49085 AN: 151618 Hom.: 8129 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.324 AC: 49157 AN: 151736 Hom.: 8148 Cov.: 31 AF XY: 0.328 AC XY: 24299 AN XY: 74120

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.324

Alfa AF: 0.297 Hom.: 9610

Bravo AF: 0.330

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7932964; hg19: chr11-2070570;