chr6-7988677-T-C

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

2

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

Genome browser will be placed here

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
PIP5K1P1NR_027712.1 linkn.2576T>C non_coding_transcript_exon_variant 1/1
BLOC1S5-TXNDC5NR_037616.1 linkn.422+37690A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BLOC1S5-TXNDC5ENST00000439343.2 linkn.372+37690A>G intron_variant 2 ENSP00000454697.1 H3BN57

Frequencies

GnomAD3 genomes
AF:
0.239
AC:
36180
AN:
151636
Hom.:
5285
Cov.:
31
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.:
31
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
14
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.

Other links and lift over

dbSNP: rs7744601; hg19: chr6-7988910; API