17-36093150-A-T

Variant names:

• chr17-36093150-A-T
• rs1634502

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 0.383 in 152,058 control chromosomes in the GnomAD database, including 11,469 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 0.38 (11469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.774
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 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: 0.383 AC: 58138 AN: 151940 Hom.: 11446 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.383 AC: 58183 AN: 152058 Hom.: 11469 Cov.: 32 AF XY: 0.385 AC XY: 28637 AN XY: 74324

African (AFR) AF: 0.285 AC: 11808 AN: 41472

American (AMR) AF: 0.479 AC: 7320 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3466

East Asian (EAS) AF: 0.474 AC: 2449 AN: 5170

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4810

European-Finnish (FIN) AF: 0.467 AC: 4942 AN: 10578

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.397 AC: 26963 AN: 67980

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.262 Hom.: 658

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.40
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1634502; hg19: chr17-34420498;