17-78212770-C-T

Variant names:

• chr17-78212770-C-T
• rs3764383

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 0.759 in 151,902 control chromosomes in the GnomAD database, including 44,174 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 0.76 (44174 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.759 AC: 115199 AN: 151784 Hom.: 44132 Cov.: 30

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.759 AC: 115295 AN: 151902 Hom.: 44174 Cov.: 30 AF XY: 0.758 AC XY: 56263 AN XY: 74204

African (AFR) AF: 0.863 AC: 35763 AN: 41442

American (AMR) AF: 0.810 AC: 12354 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2688 AN: 3470

East Asian (EAS) AF: 0.757 AC: 3903 AN: 5154

South Asian (SAS) AF: 0.749 AC: 3605 AN: 4812

European-Finnish (FIN) AF: 0.708 AC: 7462 AN: 10540

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47207 AN: 67932

Other (OTH) AF: 0.773 AC: 1623 AN: 2100

Alfa AF: 0.721 Hom.: 71534

Bravo AF: 0.774

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs3764383; hg19: chr17-76208851;