17-53152571-G-T

Variant names:

• chr17-53152571-G-T
• rs807131

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 0.792 in 151,514 control chromosomes in the GnomAD database, including 48,347 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 0.79 (48347 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 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: 0.792 AC: 119876 AN: 151398 Hom.: 48314 Cov.: 31

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.786

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.792 AC: 119953 AN: 151514 Hom.: 48347 Cov.: 31 AF XY: 0.795 AC XY: 58813 AN XY: 74008

African (AFR) AF: 0.623 AC: 25737 AN: 41302

American (AMR) AF: 0.853 AC: 13003 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2969 AN: 3466

East Asian (EAS) AF: 0.739 AC: 3765 AN: 5098

South Asian (SAS) AF: 0.830 AC: 3996 AN: 4816

European-Finnish (FIN) AF: 0.878 AC: 9193 AN: 10476

Middle Eastern (MID) AF: 0.780 AC: 223 AN: 286

European-Non Finnish (NFE) AF: 0.864 AC: 58550 AN: 67804

Other (OTH) AF: 0.802 AC: 1693 AN: 2112

Alfa AF: 0.798 Hom.: 2658

Bravo AF: 0.783

Asia WGS AF: 0.773 AC: 2688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.027
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs807131; hg19: chr17-51229932;