ENST00000849012.1:n.385-15243T>C

Variant names:

• chr12-58481915-A-G
• rs6581191
• ENST00000849012.1:n.385-15243T>C

Variant summary

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

The ENST00000849012.1(ENSG00000310312):​n.385-15243T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,038 control chromosomes in the GnomAD database, including 14,856 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 0.44 (14856 hom., cov: 32)
• Consequence: ENSG00000310312 ENST00000849012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 5 publications found

Genes affected

ENSG00000310312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849012.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310312	ENST00000849012.1		n.385-15243T>C		intron	N/A
	ENSG00000310312	ENST00000849013.1		n.244-2244T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66169 AN: 151920 Hom.: 14850 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.436 AC: 66215 AN: 152038 Hom.: 14856 Cov.: 32 AF XY: 0.435 AC XY: 32354 AN XY: 74340

African (AFR) AF: 0.368 AC: 15263 AN: 41448

American (AMR) AF: 0.368 AC: 5623 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3472

East Asian (EAS) AF: 0.644 AC: 3324 AN: 5160

South Asian (SAS) AF: 0.416 AC: 2000 AN: 4812

European-Finnish (FIN) AF: 0.516 AC: 5450 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32131 AN: 67974

Other (OTH) AF: 0.404 AC: 855 AN: 2114

Alfa AF: 0.448 Hom.: 26610

Bravo AF: 0.422

Asia WGS AF: 0.539 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs6581191; hg19: chr12-58875698;