rs13149928

Variant names:

• chr4-177672114-T-C
• rs13149928
• ENST00000507023.1:n.872-3723T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-177672114-T-C
• chr4-177672114-T-G

Variant summary

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

The ENST00000507023.1(AGA-DT):​n.872-3723T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 151,994 control chromosomes in the GnomAD database, including 42,858 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 0.75 (42858 hom., cov: 31)
• Consequence: AGA-DT ENST00000507023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 4 publications found

Genes affected

AGA-DT (HGNC:27730): (AGA divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGA-DT	NR_183777.1	n.766-24426T>C		intron_variant	Intron 4 of 4
AGA-DT	NR_183778.1	n.650-3723T>C		intron_variant	Intron 3 of 5
AGA-DT	NR_183779.1	n.650-24426T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGA-DT	ENST00000507023.1	n.872-3723T>C		intron_variant	Intron 5 of 5	2
AGA-DT	ENST00000654463.1	n.354-3723T>C		intron_variant	Intron 4 of 4
AGA-DT	ENST00000671080.1	n.141-3723T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114012 AN: 151874 Hom.: 42847 Cov.: 31

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.751 AC: 114074 AN: 151994 Hom.: 42858 Cov.: 31 AF XY: 0.751 AC XY: 55772 AN XY: 74270

African (AFR) AF: 0.740 AC: 30666 AN: 41456

American (AMR) AF: 0.791 AC: 12071 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2435 AN: 3472

East Asian (EAS) AF: 0.782 AC: 4021 AN: 5144

South Asian (SAS) AF: 0.823 AC: 3965 AN: 4820

European-Finnish (FIN) AF: 0.762 AC: 8035 AN: 10540

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.742 AC: 50475 AN: 67990

Other (OTH) AF: 0.746 AC: 1575 AN: 2112

Alfa AF: 0.746 Hom.: 176223

Bravo AF: 0.753

Asia WGS AF: 0.803 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs13149928; hg19: chr4-178593268;