chr2-203852990-G-T

Variant names:

• chr2-203852990-G-T
• rs11571293

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 0.406 in 149,260 control chromosomes in the GnomAD database, including 12,501 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 0.41 (12501 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.406 AC: 60617 AN: 149152 Hom.: 12497 Cov.: 24

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.406 AC: 60661 AN: 149260 Hom.: 12501 Cov.: 24 AF XY: 0.404 AC XY: 29312 AN XY: 72602

African (AFR) AF: 0.431 AC: 17402 AN: 40394

American (AMR) AF: 0.418 AC: 6257 AN: 14974

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1644 AN: 3460

East Asian (EAS) AF: 0.243 AC: 1230 AN: 5054

South Asian (SAS) AF: 0.557 AC: 2615 AN: 4696

European-Finnish (FIN) AF: 0.308 AC: 3071 AN: 9976

Middle Eastern (MID) AF: 0.500 AC: 145 AN: 290

European-Non Finnish (NFE) AF: 0.400 AC: 26994 AN: 67452

Other (OTH) AF: 0.447 AC: 923 AN: 2064

Alfa AF: 0.383 Hom.: 4438

Bravo AF: 0.410

Asia WGS AF: 0.454 AC: 1577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.34
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs11571293; hg19: chr2-204717713;