17-387876-T-C

Variant names:

• chr17-387876-T-C
• rs11150880

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 0.439 in 152,210 control chromosomes in the GnomAD database, including 17,206 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 0.44 (17206 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66743 AN: 152092 Hom.: 17201 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.439 AC: 66748 AN: 152210 Hom.: 17206 Cov.: 33 AF XY: 0.445 AC XY: 33147 AN XY: 74408

African (AFR) AF: 0.149 AC: 6174 AN: 41552

American (AMR) AF: 0.502 AC: 7672 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1778 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2332 AN: 5176

South Asian (SAS) AF: 0.501 AC: 2418 AN: 4830

European-Finnish (FIN) AF: 0.634 AC: 6707 AN: 10580

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38080 AN: 67990

Other (OTH) AF: 0.474 AC: 1002 AN: 2114

Alfa AF: 0.516 Hom.: 14430

Bravo AF: 0.414

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.89
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs11150880; hg19: chr17-237667; COSMIC: COSV73829950;