rs11761662

chr7-128410363-A-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 0.0838 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;