17-63899888-T-C

Variant names:

• chr17-63899888-T-C
• rs2854160
• ENST00000791137.1:n.265+4716T>C

Variant summary

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

The ENST00000791137.1(ENSG00000303015):​n.265+4716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,734 control chromosomes in the GnomAD database, including 36,097 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 0.68 (36097 hom., cov: 32)
• Consequence: ENSG00000303015 ENST00000791137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 29 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 = 0.787 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
ENSG00000303015	ENST00000791137.1	n.265+4716T>C		intron_variant	Intron 1 of 1
ENSG00000303015	ENST00000791138.1	n.220-750T>C		intron_variant	Intron 1 of 2
ENSG00000303015	ENST00000791139.1	n.193-750T>C		intron_variant	Intron 1 of 2
ENSG00000303015	ENST00000791140.1	n.143-750T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103203 AN: 151616 Hom.: 36050 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.681 AC: 103299 AN: 151734 Hom.: 36097 Cov.: 32 AF XY: 0.670 AC XY: 49632 AN XY: 74132

African (AFR) AF: 0.794 AC: 32932 AN: 41452

American (AMR) AF: 0.608 AC: 9238 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2513 AN: 5160

South Asian (SAS) AF: 0.424 AC: 2039 AN: 4808

European-Finnish (FIN) AF: 0.562 AC: 5906 AN: 10518

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45737 AN: 67826

Other (OTH) AF: 0.687 AC: 1449 AN: 2110

Alfa AF: 0.674 Hom.: 102403

Bravo AF: 0.693

Asia WGS AF: 0.479 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.055
DANN	Benign	0.19
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2854160; hg19: chr17-61977248;