13-106649072-A-T

Variant names:

• chr13-106649072-A-T
• rs1986664
• ENST00000663663.1:n.91-48185A>T

Variant summary

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

The ENST00000663663.1(ARGLU1-DT):​n.91-48185A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 151,978 control chromosomes in the GnomAD database, including 39,978 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 0.72 (39978 hom., cov: 31)
• Consequence: ARGLU1-DT ENST00000663663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 4 publications found

Genes affected

ARGLU1-DT (HGNC:43691): (ARGLU1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663663.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARGLU1-DT	ENST00000663663.1		n.91-48185A>T		intron	N/A
	ARGLU1-DT	ENST00000667614.1		n.133-48185A>T		intron	N/A
	ARGLU1-DT	ENST00000715699.1		n.241-19574A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109733 AN: 151860 Hom.: 39947 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.723 AC: 109818 AN: 151978 Hom.: 39978 Cov.: 31 AF XY: 0.731 AC XY: 54292 AN XY: 74272

African (AFR) AF: 0.733 AC: 30384 AN: 41456

American (AMR) AF: 0.718 AC: 10966 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2222 AN: 3468

East Asian (EAS) AF: 0.936 AC: 4835 AN: 5166

South Asian (SAS) AF: 0.828 AC: 3975 AN: 4802

European-Finnish (FIN) AF: 0.756 AC: 7989 AN: 10572

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47117 AN: 67940

Other (OTH) AF: 0.720 AC: 1514 AN: 2104

Alfa AF: 0.705 Hom.: 4695

Bravo AF: 0.718

Asia WGS AF: 0.853 AC: 2965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1986664; hg19: chr13-107301420;