ENST00000658746.1:n.135+12953A>G

Variant names:

• chr5-34258360-A-G
• rs2148575
• ENST00000658746.1:n.135+12953A>G

Variant summary

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

The ENST00000658746.1(ENSG00000286543):​n.135+12953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 151,654 control chromosomes in the GnomAD database, including 54,605 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 0.82 (54605 hom., cov: 29)
• Consequence: ENSG00000286543 ENST00000658746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

Genes affected

ENSG00000286543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658746.1. 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
	ENSG00000286543	ENST00000658746.1		n.135+12953A>G		intron	N/A
	ENSG00000286543	ENST00000736918.1		n.237+12953A>G		intron	N/A
	ENSG00000286543	ENST00000736919.1		n.233+12953A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124341 AN: 151536 Hom.: 54597 Cov.: 29

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.820 AC: 124381 AN: 151654 Hom.: 54605 Cov.: 29 AF XY: 0.822 AC XY: 60908 AN XY: 74088

African (AFR) AF: 0.469 AC: 19375 AN: 41312

American (AMR) AF: 0.931 AC: 14183 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4585 AN: 5170

South Asian (SAS) AF: 0.945 AC: 4531 AN: 4796

European-Finnish (FIN) AF: 0.902 AC: 9442 AN: 10466

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 65988 AN: 67888

Other (OTH) AF: 0.863 AC: 1822 AN: 2112

Alfa AF: 0.925 Hom.: 27084

Bravo AF: 0.805

Asia WGS AF: 0.902 AC: 3123 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2148575; hg19: chr5-34258465;