rs12950390

Variant names:

• chr17-47753582-T-C
• rs12950390

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 0.24 in 152,172 control chromosomes in the GnomAD database, including 4,555 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 0.24 (4555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 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: 0.240 AC: 36555 AN: 152054 Hom.: 4553 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0717

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.240 AC: 36575 AN: 152172 Hom.: 4555 Cov.: 32 AF XY: 0.240 AC XY: 17892 AN XY: 74398

African (AFR) AF: 0.243 AC: 10085 AN: 41512

American (AMR) AF: 0.236 AC: 3604 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3470

East Asian (EAS) AF: 0.0718 AC: 372 AN: 5178

South Asian (SAS) AF: 0.342 AC: 1652 AN: 4830

European-Finnish (FIN) AF: 0.220 AC: 2330 AN: 10582

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16920 AN: 67994

Other (OTH) AF: 0.230 AC: 487 AN: 2114

Alfa AF: 0.246 Hom.: 14932

Bravo AF: 0.238

Asia WGS AF: 0.214 AC: 750 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	0.41
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12950390; hg19: chr17-45830948;