17-74840873-C-T

Variant names:

• chr17-74840873-C-T
• rs1568447

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 0.517 in 151,960 control chromosomes in the GnomAD database, including 21,994 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 0.52 (21994 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 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: 0.517 AC: 78518 AN: 151842 Hom.: 21995 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.517 AC: 78525 AN: 151960 Hom.: 21994 Cov.: 31 AF XY: 0.517 AC XY: 38382 AN XY: 74290

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.630

Gnomad4 OTH AF: 0.495

Alfa AF: 0.594 Hom.: 42118

Bravo AF: 0.502

Asia WGS AF: 0.359 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.074
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1568447; hg19: chr17-72837012;