17-50758836-C-T

Variant names:

• chr17-50758836-C-T
• rs1984555

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 0.0991 in 152,056 control chromosomes in the GnomAD database, including 864 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 0.099 (864 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 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: 0.0991 AC: 15056 AN: 151938 Hom.: 860 Cov.: 30

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0991 AC: 15069 AN: 152056 Hom.: 864 Cov.: 30 AF XY: 0.0977 AC XY: 7263 AN XY: 74312

African (AFR) AF: 0.100 AC: 4145 AN: 41456

American (AMR) AF: 0.167 AC: 2546 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3470

East Asian (EAS) AF: 0.171 AC: 884 AN: 5170

South Asian (SAS) AF: 0.110 AC: 532 AN: 4822

European-Finnish (FIN) AF: 0.0252 AC: 266 AN: 10572

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.0910 AC: 6186 AN: 67992

Other (OTH) AF: 0.0989 AC: 208 AN: 2104

Alfa AF: 0.0964 Hom.: 1639

Bravo AF: 0.112

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.78
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs1984555; hg19: chr17-48836197;