2-100698011-G-T

Variant names:

• chr2-100698011-G-T
• rs1513625

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 0.184 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.228 AC: 9458 AN: 41442

American (AMR) AF: 0.118 AC: 1800 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 536 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1280 AN: 5172

South Asian (SAS) AF: 0.345 AC: 1660 AN: 4810

European-Finnish (FIN) AF: 0.131 AC: 1388 AN: 10558

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11214 AN: 67960

Other (OTH) AF: 0.184 AC: 388 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.36
PhyloP100		-0.81

Splicing

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

Other links and lift over

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