ENST00000758621.1:n.99-3197G>A

Variant names:

• chr1-72913906-G-A
• rs10493513
• ENST00000758621.1:n.99-3197G>A

Variant summary

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

The ENST00000758621.1(ENSG00000298890):​n.99-3197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,808 control chromosomes in the GnomAD database, including 13,375 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 0.38 (13375 hom., cov: 32)
• Consequence: ENSG00000298890 ENST00000758621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 3 publications found

Genes affected

ENSG00000298890 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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
ENSG00000298890	ENST00000758621.1	n.99-3197G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57705 AN: 151690 Hom.: 13385 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.380 AC: 57700 AN: 151808 Hom.: 13375 Cov.: 32 AF XY: 0.383 AC XY: 28434 AN XY: 74180

African (AFR) AF: 0.116 AC: 4814 AN: 41458

American (AMR) AF: 0.495 AC: 7528 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3470

East Asian (EAS) AF: 0.171 AC: 879 AN: 5138

South Asian (SAS) AF: 0.382 AC: 1842 AN: 4822

European-Finnish (FIN) AF: 0.552 AC: 5809 AN: 10532

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33803 AN: 67882

Other (OTH) AF: 0.382 AC: 804 AN: 2102

Alfa AF: 0.428 Hom.: 2075

Bravo AF: 0.366

Asia WGS AF: 0.261 AC: 908 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.36
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10493513; hg19: chr1-73379589;