Variant chr6-7988677-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323

Variant links:

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]

BLOC1S5-TXNDC5 links:

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

PIP5K1P1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP5K1P1	NR_027712.1 link	n.2576T>C		non_coding_transcript_exon_variant	1/1
BLOC1S5-TXNDC5	NR_037616.1 link	n.422+37690A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2 link	n.372+37690A>G		intron_variant		2		ENSP00000454697.1		H3BN57

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36180

AN:

151636

Hom.:

5285

Cov.:

show subpopulations

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.:

AF XY:

0.234

AC XY:

17366

AN XY:

74144

show subpopulations

Gnomad4 AFR

AF:

0.410

Gnomad4 AMR

AF:

0.218

Gnomad4 ASJ

AF:

0.146

Gnomad4 EAS

AF:

0.0766

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.135

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.0866

Hom.:

114

Bravo

AF:

0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

DANN

Benign

0.80

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over