rs940339

Variant names:

• chr2-227820546-T-C
• rs940339

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 0.415 in 152,082 control chromosomes in the GnomAD database, including 14,152 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 0.42 (14152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63146 AN: 151964 Hom.: 14151 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.415 AC: 63147 AN: 152082 Hom.: 14152 Cov.: 32 AF XY: 0.412 AC XY: 30636 AN XY: 74332

African (AFR) AF: 0.251 AC: 10402 AN: 41480

American (AMR) AF: 0.478 AC: 7310 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3466

East Asian (EAS) AF: 0.206 AC: 1062 AN: 5156

South Asian (SAS) AF: 0.379 AC: 1831 AN: 4826

European-Finnish (FIN) AF: 0.441 AC: 4665 AN: 10580

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34838 AN: 67976

Other (OTH) AF: 0.429 AC: 906 AN: 2112

Alfa AF: 0.481 Hom.: 33514

Bravo AF: 0.412

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.53
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs940339; hg19: chr2-228685262;