chr2-104762499-C-T

Variant names:

• chr2-104762499-C-T
• rs12615966

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 0.137 in 152,082 control chromosomes in the GnomAD database, including 1,528 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 0.14 (1528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 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: 0.138 AC: 20908 AN: 151964 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.137 AC: 20901 AN: 152082 Hom.: 1528 Cov.: 32 AF XY: 0.139 AC XY: 10303 AN XY: 74340

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0997

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.0784

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.147

Alfa AF: 0.138 Hom.: 2522

Bravo AF: 0.137

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12615966; hg19: chr2-105378957; COSMIC: COSV69871903;