17-78214076-C-T

Position:

• chr17-78214076-C-T

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 0.0879 in 513,782 control chromosomes in the GnomAD database, including 2,636 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 0.076 (638 hom., cov: 32)
  • Exomes 𝑓: 0.093 (1998 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0763 AC: 11602 AN: 152090 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0497

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.107

GnomAD4 exome AF: 0.0928 AC: 33570 AN: 361574 Hom.: 1998 AF XY: 0.0931 AC XY: 17693 AN XY: 190094

Gnomad4 AFR exome AF: 0.0252

Gnomad4 AMR exome AF: 0.0787

Gnomad4 ASJ exome AF: 0.133

Gnomad4 EAS exome AF: 0.000225

Gnomad4 SAS exome AF: 0.0764

Gnomad4 FIN exome AF: 0.0442

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.0957

GnomAD4 genome AF: 0.0762 AC: 11595 AN: 152208 Hom.: 638 Cov.: 32 AF XY: 0.0733 AC XY: 5456 AN XY: 74432

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.0966

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0808

Gnomad4 FIN AF: 0.0394

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0811 Hom.: 77

Bravo AF: 0.0767

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	10
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17878467; hg19: chr17-76210157;