ENST00000759058.1:n.149-8676T>C

Variant names:

• chr1-163471496-T-C
• rs4076764
• ENST00000759058.1:n.149-8676T>C

Variant summary

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

The ENST00000759058.1(ENSG00000298925):​n.149-8676T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,056 control chromosomes in the GnomAD database, including 9,096 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 0.33 (9096 hom., cov: 32)
• Consequence: ENSG00000298925 ENST00000759058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 3 publications found

Genes affected

ENSG00000298925 (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 (EAS) allele frequency at 95% confidence interval = 0.651 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
ENSG00000298925	ENST00000759058.1	n.149-8676T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49427 AN: 151938 Hom.: 9090 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.325 AC: 49453 AN: 152056 Hom.: 9096 Cov.: 32 AF XY: 0.337 AC XY: 25007 AN XY: 74310

African (AFR) AF: 0.179 AC: 7432 AN: 41508

American (AMR) AF: 0.369 AC: 5625 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1508 AN: 3472

East Asian (EAS) AF: 0.669 AC: 3443 AN: 5144

South Asian (SAS) AF: 0.564 AC: 2718 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4054 AN: 10564

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23589 AN: 67972

Other (OTH) AF: 0.355 AC: 751 AN: 2114

Alfa AF: 0.355 Hom.: 15444

Bravo AF: 0.313

Asia WGS AF: 0.544 AC: 1893 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	3.7
DANN	Benign	0.70
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs4076764; hg19: chr1-163441286;