rs12950743

Variant names:

• chr17-39892980-T-C
• rs12950743

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 0.451 in 151,984 control chromosomes in the GnomAD database, including 15,768 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 0.45 (15768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.451 AC: 68483 AN: 151866 Hom.: 15749 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.451 AC: 68550 AN: 151984 Hom.: 15768 Cov.: 31 AF XY: 0.452 AC XY: 33575 AN XY: 74274

African (AFR) AF: 0.389 AC: 16141 AN: 41448

American (AMR) AF: 0.421 AC: 6426 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1402 AN: 5174

South Asian (SAS) AF: 0.388 AC: 1866 AN: 4814

European-Finnish (FIN) AF: 0.572 AC: 6050 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33525 AN: 67934

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.471 Hom.: 49571

Bravo AF: 0.430

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12950743; hg19: chr17-38049233;