rs950017

Variant names:

• chr12-87466803-T-C
• rs950017

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 0.176 in 151,926 control chromosomes in the GnomAD database, including 2,563 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 0.18 (2563 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.176 AC: 26728 AN: 151808 Hom.: 2566 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.176 AC: 26738 AN: 151926 Hom.: 2563 Cov.: 33 AF XY: 0.179 AC XY: 13285 AN XY: 74272

African (AFR) AF: 0.126 AC: 5230 AN: 41468

American (AMR) AF: 0.189 AC: 2879 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3462

East Asian (EAS) AF: 0.399 AC: 2058 AN: 5162

South Asian (SAS) AF: 0.177 AC: 852 AN: 4822

European-Finnish (FIN) AF: 0.209 AC: 2214 AN: 10576

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12184 AN: 67890

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.173 Hom.: 308

Bravo AF: 0.174

Asia WGS AF: 0.275 AC: 953 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.51
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs950017; hg19: chr12-87860580;