17-63498748-T-C

Variant names:

• chr17-63498748-T-C
• rs9896208
• ENST00000577647.2:n.1969+1763T>C

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.1969+1763T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,976 control chromosomes in the GnomAD database, including 25,236 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 0.57 (25236 hom., cov: 31)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921
• Publications: 6 publications found

Genes affected

ENSG00000264813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.644 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
ENSG00000264813	ENST00000577647.2	n.1969+1763T>C		intron_variant	Intron 13 of 30	2		ENSP00000464149.1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86622 AN: 151858 Hom.: 25199 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.571 AC: 86707 AN: 151976 Hom.: 25236 Cov.: 31 AF XY: 0.574 AC XY: 42680 AN XY: 74300

African (AFR) AF: 0.445 AC: 18412 AN: 41412

American (AMR) AF: 0.612 AC: 9349 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3095 AN: 5158

South Asian (SAS) AF: 0.663 AC: 3189 AN: 4812

European-Finnish (FIN) AF: 0.664 AC: 7008 AN: 10560

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.622 AC: 42290 AN: 67976

Other (OTH) AF: 0.549 AC: 1158 AN: 2110

Alfa AF: 0.569 Hom.: 15696

Bravo AF: 0.553

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.65
PhyloP100		0.92
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs9896208; hg19: chr17-61576109;