rs11761662

Variant names:

• chr7-128410363-A-G
• rs11761662

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 0.0838 in 153,350 control chromosomes in the GnomAD database, including 723 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 0.084 (720 hom., cov: 33)
  • Exomes 𝑓: 0.089 (3 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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: 0.0838 AC: 12752 AN: 152150 Hom.: 720 Cov.: 33

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0723

GnomAD4 exome AF: 0.0887 AC: 96 AN: 1082 Hom.: 3 AF XY: 0.0873 AC XY: 51 AN XY: 584

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.107

Gnomad4 ASJ exome AF: 0.0690

Gnomad4 EAS exome AF: 0.0667

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.156

Gnomad4 NFE exome AF: 0.0942

Gnomad4 OTH exome AF: 0.0750

GnomAD4 genome AF: 0.0837 AC: 12751 AN: 152268 Hom.: 720 Cov.: 33 AF XY: 0.0846 AC XY: 6294 AN XY: 74440

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0711

Alfa AF: 0.107 Hom.: 436

Bravo AF: 0.0724

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11761662; hg19: chr7-128050417;