ENST00000439343.2:n.372+17565A>T

Variant names:

• chr6-8008802-T-A
• rs9392182
• ENST00000439343.2:n.372+17565A>T

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.372+17565A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,920 control chromosomes in the GnomAD database, including 42,718 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 0.74 (42718 hom., cov: 30)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

BLOC1S5-TXNDC5 (HGNC:42001): (BLOC1S5-TXNDC5 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring MUTED (muted homolog) and TXNDC5 (thioredoxin domain containing 5) genes on chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+17565A>T		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.372+17565A>T		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112374 AN: 151802 Hom.: 42698 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.740 AC: 112438 AN: 151920 Hom.: 42718 Cov.: 30 AF XY: 0.743 AC XY: 55190 AN XY: 74252

African (AFR) AF: 0.564 AC: 23363 AN: 41392

American (AMR) AF: 0.788 AC: 12034 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.965 AC: 5000 AN: 5184

South Asian (SAS) AF: 0.782 AC: 3771 AN: 4820

European-Finnish (FIN) AF: 0.837 AC: 8788 AN: 10494

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54612 AN: 67976

Other (OTH) AF: 0.711 AC: 1503 AN: 2114

Alfa AF: 0.764 Hom.: 5603

Bravo AF: 0.729

Asia WGS AF: 0.867 AC: 3012 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.69
PhyloP100		0.090
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

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Other links and lift over

dbSNP: rs9392182; hg19: chr6-8009035;