2-203687247-C-T

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 0.0755 in 152,188 control chromosomes in the GnomAD database, including 626 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 0.075 (626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11474 AN: 152070 Hom.: 620 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0755 AC: 11483 AN: 152188 Hom.: 626 Cov.: 32 AF XY: 0.0773 AC XY: 5749 AN XY: 74406

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0256

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0484

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0779 Hom.: 272

Bravo AF: 0.0697

Asia WGS AF: 0.0250 AC: 87 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	0.016
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11681040; hg19: chr2-204551970;