17-17030090-T-C

Position:

• chr17-17030090-T-C

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 0.8 in 151,752 control chromosomes in the GnomAD database, including 48,683 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 0.80 (48683 hom., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17030090T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287114	ENST00000659709.1	n.473+1107T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121298 AN: 151634 Hom.: 48649 Cov.: 29

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.800 AC: 121385 AN: 151752 Hom.: 48683 Cov.: 29 AF XY: 0.805 AC XY: 59716 AN XY: 74164

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.772

Alfa AF: 0.784 Hom.: 28979

Bravo AF: 0.790

Asia WGS AF: 0.818 AC: 2842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11867934; hg19: chr17-16933404;