ENST00000753311.1:n.149-2079G>C

Variant names:

• chr13-106403619-C-G
• rs10492639
• ENST00000753311.1:n.149-2079G>C

Variant summary

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

The ENST00000753311.1(ENSG00000298145):​n.149-2079G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,114 control chromosomes in the GnomAD database, including 9,065 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 (9065 hom., cov: 33)
• Consequence: ENSG00000298145 ENST00000753311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

Genes affected

ENSG00000298145 (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 (NFE) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753311.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298145	ENST00000753311.1		n.149-2079G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50414 AN: 151996 Hom.: 9070 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.331 AC: 50412 AN: 152114 Hom.: 9065 Cov.: 33 AF XY: 0.327 AC XY: 24295 AN XY: 74362

African (AFR) AF: 0.209 AC: 8692 AN: 41506

American (AMR) AF: 0.304 AC: 4636 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3472

East Asian (EAS) AF: 0.124 AC: 644 AN: 5180

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4814

European-Finnish (FIN) AF: 0.399 AC: 4217 AN: 10560

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.422 AC: 28675 AN: 67994

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.364 Hom.: 1306

Bravo AF: 0.319

Asia WGS AF: 0.178 AC: 619 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.57
DANN	Benign	0.34
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10492639; hg19: chr13-107055967;