rs12940923

Variant names:

• chr17-58292488-A-T
• rs12940923

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 0.127 in 152,182 control chromosomes in the GnomAD database, including 1,391 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 0.13 (1391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.127 AC: 19298 AN: 152064 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.127 AC: 19298 AN: 152182 Hom.: 1391 Cov.: 32 AF XY: 0.124 AC XY: 9263 AN XY: 74406

Gnomad4 AFR AF: 0.0806

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0359

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.155

Alfa AF: 0.134 Hom.: 166

Bravo AF: 0.127

Asia WGS AF: 0.0250 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12940923; hg19: chr17-56369849;