rs10496711

Positions:

• chr2-133759171-C-G
• chr2-133759171-C-T

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 0.437 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.425

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496711; hg19: chr2-134516742;