rs11682769

Variant names:

• chr2-7221149-T-C
• rs11682769

Your query was ambiguous. Multiple possible variants found:

• chr2-7221149-T-C
• chr2-7221149-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 0.354 in 152,062 control chromosomes in the GnomAD database, including 10,028 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 0.35 (10028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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: 0.354 AC: 53740 AN: 151942 Hom.: 9998 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.354 AC: 53802 AN: 152062 Hom.: 10028 Cov.: 32 AF XY: 0.356 AC XY: 26470 AN XY: 74340

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.343

Alfa AF: 0.319 Hom.: 15520

Bravo AF: 0.339

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11682769; hg19: chr2-7361280;