17-36107252-C-T

Variant names:

• chr17-36107252-C-T
• rs1619526

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 0.205 in 151,882 control chromosomes in the GnomAD database, including 3,483 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 0.21 (3483 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 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: 0.205 AC: 31156 AN: 151764 Hom.: 3481 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.205 AC: 31166 AN: 151882 Hom.: 3483 Cov.: 31 AF XY: 0.203 AC XY: 15044 AN XY: 74206

African (AFR) AF: 0.126 AC: 5235 AN: 41416

American (AMR) AF: 0.214 AC: 3263 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1546 AN: 5148

South Asian (SAS) AF: 0.230 AC: 1103 AN: 4806

European-Finnish (FIN) AF: 0.170 AC: 1785 AN: 10518

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16847 AN: 67948

Other (OTH) AF: 0.212 AC: 449 AN: 2114

Alfa AF: 0.222 Hom.: 521

Bravo AF: 0.208

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1619526; hg19: chr17-34434645;