chr2-203842694-C-T

Variant names:

• chr2-203842694-C-T
• rs231799

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.516 in 151,982 control chromosomes in the GnomAD database, including 20,611 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 0.52 (20611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.516 AC: 78296 AN: 151864 Hom.: 20590 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.516 AC: 78372 AN: 151982 Hom.: 20611 Cov.: 32 AF XY: 0.520 AC XY: 38638 AN XY: 74292

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.475

Alfa AF: 0.487 Hom.: 7477

Bravo AF: 0.508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.070
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231799; hg19: chr2-204707417;