17-36031260-C-T

Variant names:

• chr17-36031260-C-T
• rs712046

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 0.548 in 152,078 control chromosomes in the GnomAD database, including 23,321 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 0.55 (23321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.811 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: 0.548 AC: 83303 AN: 151960 Hom.: 23290 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.548 AC: 83379 AN: 152078 Hom.: 23321 Cov.: 32 AF XY: 0.553 AC XY: 41127 AN XY: 74332

African (AFR) AF: 0.536 AC: 22245 AN: 41470

American (AMR) AF: 0.598 AC: 9148 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4304 AN: 5174

South Asian (SAS) AF: 0.615 AC: 2963 AN: 4818

European-Finnish (FIN) AF: 0.517 AC: 5461 AN: 10562

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35215 AN: 67978

Other (OTH) AF: 0.555 AC: 1173 AN: 2114

Alfa AF: 0.525 Hom.: 6360

Bravo AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs712046; hg19: chr17-34358297;