rs12600940

Variant names:

• chr17-13021778-A-G
• rs12600940

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 0.482 in 152,012 control chromosomes in the GnomAD database, including 18,424 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 0.48 (18424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.715 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: 0.483 AC: 73299 AN: 151894 Hom.: 18426 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.482 AC: 73318 AN: 152012 Hom.: 18424 Cov.: 32 AF XY: 0.485 AC XY: 36036 AN XY: 74324

African (AFR) AF: 0.325 AC: 13488 AN: 41446

American (AMR) AF: 0.530 AC: 8106 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1904 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3784 AN: 5150

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4820

European-Finnish (FIN) AF: 0.526 AC: 5554 AN: 10568

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

European-Non Finnish (NFE) AF: 0.536 AC: 36454 AN: 67960

Other (OTH) AF: 0.510 AC: 1079 AN: 2114

Alfa AF: 0.490 Hom.: 2732

Bravo AF: 0.481

Asia WGS AF: 0.581 AC: 2019 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	1.6
DANN	Benign	0.55
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs12600940; hg19: chr17-12925095;