2-210704998-G-A

Variant names:

• chr2-210704998-G-A
• rs2371030

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 0.581 in 151,856 control chromosomes in the GnomAD database, including 26,831 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 0.58 (26831 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.581 AC: 88141 AN: 151736 Hom.: 26817 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.581 AC: 88185 AN: 151856 Hom.: 26831 Cov.: 31 AF XY: 0.585 AC XY: 43408 AN XY: 74184

African (AFR) AF: 0.392 AC: 16226 AN: 41374

American (AMR) AF: 0.672 AC: 10258 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2431 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4420 AN: 5146

South Asian (SAS) AF: 0.630 AC: 3039 AN: 4822

European-Finnish (FIN) AF: 0.665 AC: 6983 AN: 10506

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42919 AN: 67952

Other (OTH) AF: 0.593 AC: 1250 AN: 2108

Alfa AF: 0.602 Hom.: 50265

Bravo AF: 0.575

Asia WGS AF: 0.683 AC: 2370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.45
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs2371030; hg19: chr2-211569722;