17-17030090-T-C

Variant names:

• chr17-17030090-T-C
• rs11867934
• ENST00000659709.1:n.473+1107T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659709.1(ENSG00000287114):​n.473+1107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000287114 ENST00000659709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

Genes affected

ENSG00000287114 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287114	ENST00000659709.1	n.473+1107T>C		intron_variant	Intron 2 of 2

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;