17-75408456-C-T

Variant names:

• chr17-75408456-C-T
• rs930297

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 0.773 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.512 AC: 21198 AN: 41420

American (AMR) AF: 0.806 AC: 12310 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2914 AN: 3472

East Asian (EAS) AF: 0.912 AC: 4727 AN: 5182

South Asian (SAS) AF: 0.852 AC: 4111 AN: 4824

European-Finnish (FIN) AF: 0.933 AC: 9890 AN: 10600

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59767 AN: 68000

Other (OTH) AF: 0.778 AC: 1640 AN: 2108

Alfa AF: 0.845 Hom.: 101046

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs930297; hg19: chr17-73404537;