17-63902485-T-C

Variant names:

• chr17-63902485-T-C
• rs2955245
• ENST00000791139.1:n.494T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791139.1(ENSG00000303015):​n.494T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,028 control chromosomes in the GnomAD database, including 42,257 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 0.73 (42257 hom., cov: 32)
• Consequence: ENSG00000303015 ENST00000791139.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 8 publications found

Genes affected

ENSG00000303015 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791139.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303015	ENST00000791139.1		n.494T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000303015	ENST00000791137.1		n.265+7313T>C		intron	N/A
	ENSG00000303015	ENST00000791138.1		n.463-28T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111084 AN: 151910 Hom.: 42202 Cov.: 32

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.731 AC: 111185 AN: 152028 Hom.: 42257 Cov.: 32 AF XY: 0.718 AC XY: 53370 AN XY: 74294

African (AFR) AF: 0.928 AC: 38543 AN: 41532

American (AMR) AF: 0.654 AC: 9986 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2624 AN: 3466

East Asian (EAS) AF: 0.487 AC: 2518 AN: 5174

South Asian (SAS) AF: 0.449 AC: 2162 AN: 4820

European-Finnish (FIN) AF: 0.563 AC: 5925 AN: 10524

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46897 AN: 67940

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.711 Hom.: 4899

Bravo AF: 0.751

Asia WGS AF: 0.496 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.33
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2955245; hg19: chr17-61979845;