2-210704998-G-A

Position:

• chr2-210704998-G-A

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 0.581 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.593

Alfa AF: 0.622 Hom.: 30868

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371030; hg19: chr2-211569722;