rs10496605

Variant names:

• chr2-123042772-G-A
• rs10496605

Your query was ambiguous. Multiple possible variants found:

• chr2-123042772-G-A
• chr2-123042772-G-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 0.109 in 151,604 control chromosomes in the GnomAD database, including 2,032 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 0.11 (2032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.109 AC: 16528 AN: 151484 Hom.: 2033 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0660

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.109 AC: 16551 AN: 151604 Hom.: 2032 Cov.: 32 AF XY: 0.108 AC XY: 8035 AN XY: 74080

Gnomad4 AFR AF: 0.301 AC: 0.300532 AN: 0.300532

Gnomad4 AMR AF: 0.0598 AC: 0.0597712 AN: 0.0597712

Gnomad4 ASJ AF: 0.0254 AC: 0.0254482 AN: 0.0254482

Gnomad4 EAS AF: 0.168 AC: 0.168217 AN: 0.168217

Gnomad4 SAS AF: 0.0819 AC: 0.081875 AN: 0.081875

Gnomad4 FIN AF: 0.0179 AC: 0.0179184 AN: 0.0179184

Gnomad4 NFE AF: 0.0202 AC: 0.020184 AN: 0.020184

Gnomad4 OTH AF: 0.0905 AC: 0.0904762 AN: 0.0904762

Alfa AF: 0.0613 Hom.: 1353

Bravo AF: 0.122

Asia WGS AF: 0.135 AC: 464 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496605; hg19: chr2-123800348;