13-80829577-T-C

Variant names:

• chr13-80829577-T-C
• rs4052484
• ENST00000665186.1:n.59-10574A>G

Variant summary

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

The ENST00000665186.1(ENSG00000286746):​n.59-10574A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,132 control chromosomes in the GnomAD database, including 59,360 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 0.88 (59360 hom., cov: 32)
• Consequence: ENSG00000286746 ENST00000665186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 1 publications found

Genes affected

ENSG00000286746 (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 = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665186.1. 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
	ENSG00000286746	ENST00000665186.1		n.59-10574A>G		intron	N/A
	ENSG00000286746	ENST00000756377.1		n.56-10574A>G		intron	N/A
	ENSG00000286746	ENST00000756378.1		n.48-10574A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134005 AN: 152014 Hom.: 59309 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.838

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.882 AC: 134114 AN: 152132 Hom.: 59360 Cov.: 32 AF XY: 0.876 AC XY: 65165 AN XY: 74370

African (AFR) AF: 0.933 AC: 38758 AN: 41540

American (AMR) AF: 0.903 AC: 13800 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3065 AN: 3466

East Asian (EAS) AF: 0.767 AC: 3964 AN: 5170

South Asian (SAS) AF: 0.746 AC: 3596 AN: 4818

European-Finnish (FIN) AF: 0.812 AC: 8583 AN: 10570

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.874 AC: 59381 AN: 67978

Other (OTH) AF: 0.871 AC: 1840 AN: 2112

Alfa AF: 0.883 Hom.: 7674

Bravo AF: 0.893

Asia WGS AF: 0.770 AC: 2671 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.51
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4052484; hg19: chr13-81403712;