chr2-203889630-T-C

Variant names:

• chr2-203889630-T-C
• rs7600322

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;