chr17-54886696-T-A

Variant names:

• chr17-54886696-T-A
• rs10515083

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.458 in 151,936 control chromosomes in the GnomAD database, including 16,901 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 0.46 (16901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69531 AN: 151820 Hom.: 16899 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.458 AC: 69561 AN: 151936 Hom.: 16901 Cov.: 32 AF XY: 0.454 AC XY: 33699 AN XY: 74262

African (AFR) AF: 0.312 AC: 12900 AN: 41404

American (AMR) AF: 0.458 AC: 6994 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3464

East Asian (EAS) AF: 0.226 AC: 1169 AN: 5162

South Asian (SAS) AF: 0.469 AC: 2259 AN: 4820

European-Finnish (FIN) AF: 0.508 AC: 5358 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37395 AN: 67958

Other (OTH) AF: 0.471 AC: 996 AN: 2114

Alfa AF: 0.510 Hom.: 2584

Bravo AF: 0.445

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10515083; hg19: chr17-52964057;