2-203878211-G-T

Variant names:

• chr2-203878211-G-T
• rs11571302

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 0.424 in 151,956 control chromosomes in the GnomAD database, including 14,036 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 0.42 (14036 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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: 0.425 AC: 64465 AN: 151840 Hom.: 14031 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.424 AC: 64491 AN: 151956 Hom.: 14036 Cov.: 31 AF XY: 0.421 AC XY: 31231 AN XY: 74270

African (AFR) AF: 0.359 AC: 14884 AN: 41424

American (AMR) AF: 0.452 AC: 6918 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1502 AN: 5144

South Asian (SAS) AF: 0.615 AC: 2955 AN: 4802

European-Finnish (FIN) AF: 0.330 AC: 3478 AN: 10550

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31380 AN: 67964

Other (OTH) AF: 0.472 AC: 998 AN: 2114

Alfa AF: 0.432 Hom.: 4729

Bravo AF: 0.425

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs11571302; hg19: chr2-204742934;