rs7931342

chr11-69227030-T-G

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 0.569 in 151,944 control chromosomes in the GnomAD database, including 26,370 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 0.57 (26370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86374 AN: 151826 Hom.: 26326 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 151944 Hom.: 26370 Cov.: 32 AF XY: 0.563 AC XY: 41829 AN XY: 74240

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.574

Alfa AF: 0.523 Hom.: 33009

Bravo AF: 0.576

Asia WGS AF: 0.417 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.18
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7931342; hg19: chr11-68994497;