chr2-203967715-G-T

Variant names:

• chr2-203967715-G-T
• rs1896286

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 0.491 in 152,078 control chromosomes in the GnomAD database, including 20,567 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 0.49 (20567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74695 AN: 151960 Hom.: 20562 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.491 AC: 74721 AN: 152078 Hom.: 20567 Cov.: 32 AF XY: 0.489 AC XY: 36373 AN XY: 74342

African (AFR) AF: 0.226 AC: 9362 AN: 41488

American (AMR) AF: 0.520 AC: 7945 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3329 AN: 5156

South Asian (SAS) AF: 0.489 AC: 2361 AN: 4828

European-Finnish (FIN) AF: 0.541 AC: 5722 AN: 10576

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41916 AN: 67958

Other (OTH) AF: 0.549 AC: 1158 AN: 2108

Alfa AF: 0.586 Hom.: 113612

Bravo AF: 0.483

Asia WGS AF: 0.557 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1896286; hg19: chr2-204832438;