rs10496711

Variant names:

• chr2-133759171-C-G
• rs10496711

Your query was ambiguous. Multiple possible variants found:

• chr2-133759171-C-G
• chr2-133759171-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 0.437 in 152,018 control chromosomes in the GnomAD database, including 14,950 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 0.44 (14950 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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: 0.437 AC: 66346 AN: 151900 Hom.: 14933 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.437 AC: 66412 AN: 152018 Hom.: 14950 Cov.: 32 AF XY: 0.437 AC XY: 32494 AN XY: 74306

African (AFR) AF: 0.506 AC: 20985 AN: 41460

American (AMR) AF: 0.390 AC: 5949 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3648 AN: 5174

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4816

European-Finnish (FIN) AF: 0.366 AC: 3864 AN: 10552

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26884 AN: 67962

Other (OTH) AF: 0.425 AC: 897 AN: 2112

Alfa AF: 0.292 Hom.: 714

Bravo AF: 0.445

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.077
DANN	Benign	0.46
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10496711; hg19: chr2-134516742;