ENST00000658845.1:n.63-556C>T

Variant names:

• chr10-113486173-G-A
• rs1033772
• ENST00000658845.2:n.248-556C>T

Variant summary

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

The ENST00000658845.2(ENSG00000286289):​n.248-556C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,896 control chromosomes in the GnomAD database, including 13,889 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 0.42 (13889 hom., cov: 32)
• Consequence: ENSG00000286289 ENST00000658845.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 7 publications found

Genes affected

ENSG00000286289 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658845.2. 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
	ENSG00000286289	ENST00000658845.2		n.248-556C>T		intron	N/A
	ENSG00000286289	ENST00000793015.1		n.249-3982C>T		intron	N/A
	ENSG00000286289	ENST00000793016.1		n.284-3982C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63163 AN: 151778 Hom.: 13867 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.416 AC: 63223 AN: 151896 Hom.: 13889 Cov.: 32 AF XY: 0.423 AC XY: 31442 AN XY: 74250

African (AFR) AF: 0.471 AC: 19488 AN: 41408

American (AMR) AF: 0.565 AC: 8638 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3352 AN: 5166

South Asian (SAS) AF: 0.481 AC: 2312 AN: 4804

European-Finnish (FIN) AF: 0.385 AC: 4059 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22550 AN: 67908

Other (OTH) AF: 0.450 AC: 950 AN: 2110

Alfa AF: 0.374 Hom.: 27698

Bravo AF: 0.435

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1033772; hg19: chr10-115245932;