17-50026571-C-T

Variant names:

• chr17-50026571-C-T
• rs890397

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 0.564 in 152,010 control chromosomes in the GnomAD database, including 26,276 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 0.56 (26276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85776 AN: 151894 Hom.: 26275 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.564 AC: 85791 AN: 152010 Hom.: 26276 Cov.: 32 AF XY: 0.561 AC XY: 41659 AN XY: 74288

African (AFR) AF: 0.323 AC: 13365 AN: 41420

American (AMR) AF: 0.571 AC: 8721 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1952 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2150 AN: 5154

South Asian (SAS) AF: 0.607 AC: 2926 AN: 4818

European-Finnish (FIN) AF: 0.646 AC: 6838 AN: 10582

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47795 AN: 67982

Other (OTH) AF: 0.585 AC: 1233 AN: 2108

Alfa AF: 0.641 Hom.: 76578

Bravo AF: 0.543

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs890397; hg19: chr17-48103935;