chr2-203905331-A-G

Position:

• chr2-203905331-A-G

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 0.179 in 152,226 control chromosomes in the GnomAD database, including 2,579 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 0.18 (2579 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 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: 0.179 AC: 27180 AN: 152108 Hom.: 2576 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.179 AC: 27194 AN: 152226 Hom.: 2579 Cov.: 33 AF XY: 0.177 AC XY: 13206 AN XY: 74426

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.209

Alfa AF: 0.176 Hom.: 320

Bravo AF: 0.177

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34037980; hg19: chr2-204770054;