13-86126868-A-G

Variant names:

• chr13-86126868-A-G
• rs1413455
• ENST00000445967.1:n.149-43977A>G

Variant summary

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

The ENST00000445967.1(ENSG00000232252):​n.149-43977A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,998 control chromosomes in the GnomAD database, including 27,038 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 0.59 (27038 hom., cov: 32)
• Consequence: ENSG00000232252 ENST00000445967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 2 publications found

Genes affected

ENSG00000232252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445967.1. 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
	ENSG00000232252	ENST00000445967.1	TSL:5	n.149-43977A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89607 AN: 151882 Hom.: 27002 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.590 AC: 89691 AN: 151998 Hom.: 27038 Cov.: 32 AF XY: 0.590 AC XY: 43787 AN XY: 74278

African (AFR) AF: 0.711 AC: 29475 AN: 41484

American (AMR) AF: 0.535 AC: 8145 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1775 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2192 AN: 5140

South Asian (SAS) AF: 0.432 AC: 2084 AN: 4824

European-Finnish (FIN) AF: 0.663 AC: 7024 AN: 10588

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37141 AN: 67944

Other (OTH) AF: 0.550 AC: 1161 AN: 2110

Alfa AF: 0.553 Hom.: 11942

Bravo AF: 0.587

Asia WGS AF: 0.453 AC: 1578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1413455; hg19: chr13-86701003;