rs940339

Variant names:

• chr2-227820546-T-C
• rs940339

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 0.415 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.416 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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.429

Alfa AF: 0.491 Hom.: 25134

Bravo AF: 0.412

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs940339; hg19: chr2-228685262;