rs7395662

chr11-48497341-A-Gchr11-48497341-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 0.562 in 151,948 control chromosomes in the GnomAD database, including 24,795 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 0.56 (24794 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.62 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: 0.562 AC: 85302 AN: 151828 Hom.: 24773 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.575

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.562 AC: 85372 AN: 151946 Hom.: 24794 Cov.: 32 AF XY: 0.560 AC XY: 41604 AN XY: 74252

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.577

Alfa AF: 0.610 Hom.: 66690

Bravo AF: 0.557

Asia WGS AF: 0.432 AC: 1502 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.19
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7395662; hg19: chr11-48518893;