17-78212770-C-T

Variant names:

• chr17-78212770-C-T
• rs3764383

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.773

Alfa AF: 0.716 Hom.: 42777

Bravo AF: 0.774

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3764383; hg19: chr17-76208851;