rs11763921

Positions:

• chr7-97774965-G-A

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 0.137 in 152,138 control chromosomes in the GnomAD database, including 2,337 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 0.14 (2337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20863 AN: 152018 Hom.: 2338 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0900

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0453

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0735

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.137 AC: 20893 AN: 152138 Hom.: 2337 Cov.: 32 AF XY: 0.132 AC XY: 9817 AN XY: 74392

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.0898

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.0182

Gnomad4 FIN AF: 0.0453

Gnomad4 NFE AF: 0.0735

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0880 Hom.: 817

Bravo AF: 0.150

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
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: rs11763921; hg19: chr7-97404277;