2-210684885-C-T

Variant names:

• chr2-210684885-C-T
• rs2371015

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 0.38 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.382 AC: 15759 AN: 41268

American (AMR) AF: 0.415 AC: 6317 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1550 AN: 3460

East Asian (EAS) AF: 0.644 AC: 3308 AN: 5140

South Asian (SAS) AF: 0.358 AC: 1713 AN: 4780

European-Finnish (FIN) AF: 0.374 AC: 3938 AN: 10530

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23846 AN: 67832

Other (OTH) AF: 0.388 AC: 813 AN: 2098

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
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2371015; hg19: chr2-211549609;