2-203969532-A-G

Variant names:

• chr2-203969532-A-G
• rs3096747

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 0.492 in 151,944 control chromosomes in the GnomAD database, including 20,587 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 0.49 (20587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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: 0.492 AC: 74701 AN: 151822 Hom.: 20581 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.492 AC: 74729 AN: 151944 Hom.: 20587 Cov.: 31 AF XY: 0.490 AC XY: 36357 AN XY: 74236

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.548

Alfa AF: 0.538 Hom.: 2817

Bravo AF: 0.484

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3096747; hg19: chr2-204834255; COSMIC: COSV69623365;