rs10496601

Variant names:

• chr2-122895707-A-G
• rs10496601

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 0.0355 in 151,940 control chromosomes in the GnomAD database, including 249 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 0.036 (249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0993 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: 0.0355 AC: 5389 AN: 151822 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00320

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0355 AC: 5398 AN: 151940 Hom.: 249 Cov.: 32 AF XY: 0.0354 AC XY: 2627 AN XY: 74278

African (AFR) AF: 0.102 AC: 4221 AN: 41452

American (AMR) AF: 0.0180 AC: 274 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 266 AN: 3460

East Asian (EAS) AF: 0.00233 AC: 12 AN: 5146

South Asian (SAS) AF: 0.0686 AC: 330 AN: 4814

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10624

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00320 AC: 217 AN: 67884

Other (OTH) AF: 0.0303 AC: 64 AN: 2112

Alfa AF: 0.0228 Hom.: 52

Bravo AF: 0.0385

Asia WGS AF: 0.0450 AC: 157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10496601; hg19: chr2-123653283;