chr2-210684885-C-T

Variant names:

• chr2-210684885-C-T
• rs2371015

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 0.38 in 151,532 control chromosomes in the GnomAD database, including 11,176 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 0.38 (11176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 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: 0.380 AC: 57583 AN: 151414 Hom.: 11161 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.380 AC: 57620 AN: 151532 Hom.: 11176 Cov.: 32 AF XY: 0.381 AC XY: 28238 AN XY: 74044

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.388

Alfa AF: 0.282 Hom.: 977

Bravo AF: 0.385

Asia WGS AF: 0.442 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371015; hg19: chr2-211549609;