17-36145077-C-T

Position:

• chr17-36145077-C-T

Variant summary

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

The ENST00000617914.1(ENSG00000276241):​n.42-2503C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 150,992 control chromosomes in the GnomAD database, including 117 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 0.10 (117 hom., cov: 34)
• Consequence: ENSG00000276241 ENST00000617914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

Genes affected

ENSG00000276241 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927369	XR_007065727.1	n.85+3883G>A		intron_variant
LOC101927369	XR_007065728.1	n.85+3883G>A		intron_variant
LOC101927369	XR_243796.5	n.85+3883G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000276241	ENST00000617914.1	n.42-2503C>T		intron_variant		3
ENSG00000289485	ENST00000689280.1	n.88+3883G>A		intron_variant
ENSG00000289485	ENST00000693235.1	n.121+3883G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15292 AN: 150874 Hom.: 117 Cov.: 34

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.101 AC: 15293 AN: 150992 Hom.: 117 Cov.: 34 AF XY: 0.103 AC XY: 7567 AN XY: 73798

Gnomad4 AFR AF: 0.0310

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0477 Hom.: 6

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9910447; hg19: chr17-34472462;