rs3940409

Variant names:

• chr2-204250936-G-A
• rs3940409

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.642 in 152,140 control chromosomes in the GnomAD database, including 31,579 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 0.64 (31579 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 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: 0.642 AC: 97553 AN: 152022 Hom.: 31545 Cov.: 33

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.642 AC: 97626 AN: 152140 Hom.: 31579 Cov.: 33 AF XY: 0.644 AC XY: 47861 AN XY: 74362

African (AFR) AF: 0.588 AC: 24396 AN: 41484

American (AMR) AF: 0.602 AC: 9206 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2345 AN: 5160

South Asian (SAS) AF: 0.721 AC: 3478 AN: 4824

European-Finnish (FIN) AF: 0.766 AC: 8122 AN: 10608

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45922 AN: 67980

Other (OTH) AF: 0.601 AC: 1271 AN: 2116

Alfa AF: 0.656 Hom.: 4969

Bravo AF: 0.624

Asia WGS AF: 0.598 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.58
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs3940409; hg19: chr2-205115659;