ENST00000439343.2:n.372+37690A>G

Variant names:

• chr6-7988677-T-C
• rs7744601
• ENST00000439343.2:n.372+37690A>G

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+37690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,742 control chromosomes in the GnomAD database, including 5,294 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 0.24 (5294 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 3 publications found

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]

PIP5K1P1 (HGNC:28372): (phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439343.2. 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
	PIP5K1P1	NR_027712.1		n.2576T>C		non_coding_transcript_exon	Exon 1 of 1
	BLOC1S5-TXNDC5	NR_037616.1		n.422+37690A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLOC1S5-TXNDC5	ENST00000439343.2	TSL:2	n.372+37690A>G		intron	N/A	ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36180 AN: 151636 Hom.: 5285 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.239 AC: 36239 AN: 151742 Hom.: 5294 Cov.: 31 AF XY: 0.234 AC XY: 17366 AN XY: 74144

African (AFR) AF: 0.410 AC: 16931 AN: 41310

American (AMR) AF: 0.218 AC: 3322 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3466

East Asian (EAS) AF: 0.0766 AC: 395 AN: 5160

South Asian (SAS) AF: 0.140 AC: 673 AN: 4804

European-Finnish (FIN) AF: 0.135 AC: 1416 AN: 10478

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12076 AN: 67952

Other (OTH) AF: 0.226 AC: 476 AN: 2104

Alfa AF: 0.0866 Hom.: 114

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		-0.32
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

Other links and lift over

dbSNP: rs7744601; hg19: chr6-7988910;