chr2-100698011-G-T

Variant names:

• chr2-100698011-G-T
• rs1513625

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 0.184 in 152,000 control chromosomes in the GnomAD database, including 2,785 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 0.18 (2785 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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: 0.184 AC: 27887 AN: 151882 Hom.: 2770 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.184 AC: 27931 AN: 152000 Hom.: 2785 Cov.: 32 AF XY: 0.186 AC XY: 13800 AN XY: 74304

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.184

Alfa AF: 0.0827 Hom.: 117

Bravo AF: 0.179

Asia WGS AF: 0.325 AC: 1127 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1513625; hg19: chr2-101314473; COSMIC: COSV60085101;