17-76973346-T-C

Variant names:

• chr17-76973346-T-C
• rs4788961
• ENST00000840720.1:n.325-2568T>C

Variant summary

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

The ENST00000840720.1(ENSG00000309397):​n.325-2568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,896 control chromosomes in the GnomAD database, including 22,739 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 0.54 (22739 hom., cov: 31)
• Consequence: ENSG00000309397 ENST00000840720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 2 publications found

Genes affected

ENSG00000309397 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 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
ENSG00000309397	ENST00000840720.1	n.325-2568T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82074 AN: 151778 Hom.: 22714 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.541 AC: 82148 AN: 151896 Hom.: 22739 Cov.: 31 AF XY: 0.539 AC XY: 39992 AN XY: 74216

African (AFR) AF: 0.667 AC: 27629 AN: 41402

American (AMR) AF: 0.481 AC: 7348 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1617 AN: 3466

East Asian (EAS) AF: 0.548 AC: 2822 AN: 5152

South Asian (SAS) AF: 0.363 AC: 1744 AN: 4810

European-Finnish (FIN) AF: 0.556 AC: 5862 AN: 10538

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33368 AN: 67944

Other (OTH) AF: 0.515 AC: 1089 AN: 2114

Alfa AF: 0.504 Hom.: 86251

Bravo AF: 0.545

Asia WGS AF: 0.483 AC: 1679 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	1.2
DANN	Benign	0.20
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4788961; hg19: chr17-74969428;