dbSNP rs6597293: BLOC1S5-TXNDC5:n.372+38717C>G (chr6-7987650-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000439343.2(BLOC1S5-TXNDC5):n.372+38717C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 948,782 control chromosomes in the GnomAD database, including 48,777 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 0.38 ( 12417 hom., cov: 31)

Exomes 𝑓: 0.29 ( 36360 hom. )

Consequence

BLOC1S5-TXNDC5
ENST00000439343.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Publications

10 publications found

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000439343.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIP5K1P1	NR_027712.1		n.1549G>C		non_coding_transcript_exon	Exon 1 of 1
	BLOC1S5-TXNDC5	NR_037616.1		n.422+38717C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLOC1S5-TXNDC5	ENST00000439343.2	TSL:2	n.372+38717C>G		intron	N/A	ENSP00000454697.1	H3BN57
	PIP5K1P1	ENST00000460661.1	TSL:6	n.1114G>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.381

AC:

57888

AN:

151920

Hom.:

12400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.570

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.399

GnomAD2 exomes

AF:

0.309

AC:

77594

AN:

250994

AF XY:

0.305

show subpopulations

Gnomad AFR exome

AF:

0.579

Gnomad AMR exome

AF:

0.315

Gnomad ASJ exome

AF:

0.363

Gnomad EAS exome

AF:

0.120

Gnomad FIN exome

AF:

0.267

Gnomad NFE exome

AF:

0.316

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.291

AC:

231831

AN:

796746

Hom.:

36360

Cov.:

AF XY:

0.292

AC XY:

123107

AN XY:

422200

show subpopulations

African (AFR)

AF:

0.559

AC:

11238

AN:

20104

American (AMR)

AF:

0.319

AC:

13925

AN:

43676

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

7817

AN:

21834

East Asian (EAS)

AF:

0.105

AC:

3842

AN:

36758

South Asian (SAS)

AF:

0.258

AC:

18895

AN:

73132

European-Finnish (FIN)

AF:

0.262

AC:

13723

AN:

52470

Middle Eastern (MID)

AF:

0.449

AC:

2004

AN:

4460

European-Non Finnish (NFE)

AF:

0.293

AC:

148272

AN:

506100

Other (OTH)

AF:

0.317

AC:

12115

AN:

38212

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

9857

19714

29572

39429

49286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2430

4860

7290

9720

12150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.381

AC:

57956

AN:

152036

Hom.:

12417

Cov.:

AF XY:

0.375

AC XY:

27905

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.570

AC:

23635

AN:

41448

American (AMR)

AF:

0.348

AC:

5314

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.376

AC:

1305

AN:

3470

East Asian (EAS)

AF:

0.112

AC:

581

AN:

5170

South Asian (SAS)

AF:

0.254

AC:

1223

AN:

4816

European-Finnish (FIN)

AF:

0.265

AC:

2803

AN:

10562

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21624

AN:

67972

Other (OTH)

AF:

0.400

AC:

844

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1710

3420

5130

6840

8550

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.262

Hom.:

949

Bravo

AF:

0.399

Asia WGS

AF:

0.201

AC:

702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

7.1

(source)

DANN

Benign

0.81

PhyloP100

1.9

Mutation Taster

=97/3

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over