rs2096767

Variant names:

• chr11-102920669-C-G
• rs2096767

Your query was ambiguous. Multiple possible variants found:

• chr11-102920669-C-G
• chr11-102920669-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.367 in 152,136 control chromosomes in the GnomAD database, including 10,341 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 0.37 (10341 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.367 AC: 55728 AN: 152018 Hom.: 10333 Cov.: 33

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.367 AC: 55783 AN: 152136 Hom.: 10341 Cov.: 33 AF XY: 0.375 AC XY: 27870 AN XY: 74382

African (AFR) AF: 0.404 AC: 16771 AN: 41494

American (AMR) AF: 0.414 AC: 6337 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2368 AN: 5170

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4824

European-Finnish (FIN) AF: 0.413 AC: 4366 AN: 10574

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21676 AN: 67992

Other (OTH) AF: 0.379 AC: 801 AN: 2114

Alfa AF: 0.209 Hom.: 463

Bravo AF: 0.368

Asia WGS AF: 0.420 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.62
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2096767; hg19: chr11-102791399;