chr2-203705416-G-A

Variant names:

• chr2-203705416-G-A
• rs3181097

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 0.103 in 152,096 control chromosomes in the GnomAD database, including 1,405 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 0.10 (1405 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 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: 0.103 AC: 15618 AN: 151978 Hom.: 1399 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0970

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

GnomAD4 genome AF: 0.103 AC: 15663 AN: 152096 Hom.: 1405 Cov.: 31 AF XY: 0.106 AC XY: 7847 AN XY: 74356

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0276

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.0588

Gnomad4 NFE AF: 0.0430

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.0604 Hom.: 414

Bravo AF: 0.114

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181097; hg19: chr2-204570139;