rs13149928

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183786.1(AGA-DT):​n.359-3723T>C variant causes a intron, non coding transcript 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 NR_183786.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
AGA-DT	NR_183786.1	n.359-3723T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGA-DT	ENST00000654463.1	n.354-3723T>C		intron_variant, non_coding_transcript_variant
AGA-DT	ENST00000507023.1	n.872-3723T>C		intron_variant, non_coding_transcript_variant		2
AGA-DT	ENST00000671080.1	n.141-3723T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.746

Alfa AF: 0.745 Hom.: 83173

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13149928; hg19: chr4-178593268;