chr17-13430017-C-T

Position:

• chr17-13430017-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 0.0689 in 152,200 control chromosomes in the GnomAD database, including 531 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 0.069 (531 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 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: 0.0689 AC: 10475 AN: 152082 Hom.: 532 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0189

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0689 AC: 10484 AN: 152200 Hom.: 531 Cov.: 33 AF XY: 0.0660 AC XY: 4912 AN XY: 74456

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0498

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0189

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0560 Hom.: 37

Bravo AF: 0.0745

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517444; hg19: chr17-13333334;