chr2-102037216-G-A

Variant names:

• chr2-102037216-G-A
• rs1008394

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 0.236 in 151,920 control chromosomes in the GnomAD database, including 4,822 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 0.24 (4822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35861 AN: 151802 Hom.: 4812 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.236 AC: 35893 AN: 151920 Hom.: 4822 Cov.: 32 AF XY: 0.242 AC XY: 17929 AN XY: 74238

African (AFR) AF: 0.132 AC: 5453 AN: 41428

American (AMR) AF: 0.289 AC: 4406 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1349 AN: 5144

South Asian (SAS) AF: 0.129 AC: 623 AN: 4818

European-Finnish (FIN) AF: 0.413 AC: 4357 AN: 10550

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18167 AN: 67930

Other (OTH) AF: 0.241 AC: 508 AN: 2108

Alfa AF: 0.159 Hom.: 409

Bravo AF: 0.226

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.84
DANN	Benign	0.42
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1008394; hg19: chr2-102653678; COSMIC: COSV60085688;