17-75408456-C-T

Position:

• chr17-75408456-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 0.773 in 152,094 control chromosomes in the GnomAD database, including 47,516 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 0.77 (47516 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117496 AN: 151976 Hom.: 47507 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.773 AC: 117530 AN: 152094 Hom.: 47516 Cov.: 31 AF XY: 0.779 AC XY: 57929 AN XY: 74360

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.778

Alfa AF: 0.852 Hom.: 76478

Bravo AF: 0.752

Asia WGS AF: 0.849 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs930297; hg19: chr17-73404537;