2-203889630-T-C

Position:

• chr2-203889630-T-C

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 0.405 in 151,988 control chromosomes in the GnomAD database, including 13,493 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 (13493 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

ACMG classification

Verdict is Benign. Variant got -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 = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61623 AN: 151870 Hom.: 13500 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.405 AC: 61615 AN: 151988 Hom.: 13493 Cov.: 31 AF XY: 0.404 AC XY: 29989 AN XY: 74292

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.467

Alfa AF: 0.433 Hom.: 1837

Bravo AF: 0.400

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7600322; hg19: chr2-204754353;