chr2-200285317-C-T

Variant names:

• chr2-200285317-C-T
• rs295137

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 0.401 in 151,954 control chromosomes in the GnomAD database, including 12,576 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 0.40 (12576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 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: 0.401 AC: 60940 AN: 151836 Hom.: 12568 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.401 AC: 60969 AN: 151954 Hom.: 12576 Cov.: 32 AF XY: 0.396 AC XY: 29374 AN XY: 74246

African (AFR) AF: 0.480 AC: 19860 AN: 41414

American (AMR) AF: 0.314 AC: 4794 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1162 AN: 5176

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3777 AN: 10534

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27078 AN: 67962

Other (OTH) AF: 0.390 AC: 821 AN: 2106

Alfa AF: 0.402 Hom.: 40572

Bravo AF: 0.401

Asia WGS AF: 0.281 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	16
DANN	Benign	0.72
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs295137; hg19: chr2-201150040;