rs2940930

Variant names:

• chr5-42405409-G-A
• rs2940930

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 0.324 in 151,332 control chromosomes in the GnomAD database, including 8,716 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 0.32 (8716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

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 (EAS) allele frequency at 95% confidence interval = 0.527 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: 0.324 AC: 48955 AN: 151218 Hom.: 8719 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.324 AC: 48973 AN: 151332 Hom.: 8716 Cov.: 32 AF XY: 0.329 AC XY: 24293 AN XY: 73892

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.310

Alfa AF: 0.361 Hom.: 4749

Bravo AF: 0.315

Asia WGS AF: 0.483 AC: 1667 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.051
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2940930; hg19: chr5-42405511;