Genetic Variant ENST00000642577.1:n.448G>A (chr6-32390493-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000642577.1(TSBP1-AS1):n.448G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 154,250 control chromosomes in the GnomAD database, including 6,341 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 0.28 ( 6203 hom., cov: 32)

Exomes 𝑓: 0.22 ( 138 hom. )

Consequence

TSBP1-AS1
ENST00000642577.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320

Publications

45 publications found

Variant links:

Genes affected

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

TSBP1-AS1 links:

HCG23 (HGNC:19713): (HLA complex group 23)

HCG23 links:

Genome browser will be placed here

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSBP1-AS1	NR_136245.1 link	n.303-14961G>A		intron_variant	Intron 2 of 3
HCG23	NR_044996.1 link	n.-17G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
TSBP1-AS1	ENST00000642577.1 link	n.448G>A	non_coding_transcript_exon_variant	Exon 3 of 6
TSBP1-AS1	ENST00000644884.2 link	n.1148G>A	non_coding_transcript_exon_variant	Exon 4 of 4
TSBP1-AS1	ENST00000645134.1 link	n.367G>A	non_coding_transcript_exon_variant	Exon 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

41566

AN:

148974

Hom.:

6192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.392

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.173

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.283

GnomAD4 exome

AF:

0.222

AC:

1144

AN:

5156

Hom.:

138

Cov.:

AF XY:

0.220

AC XY:

610

AN XY:

2776

show subpopulations

African (AFR)

AF:

0.349

AC:

AN:

American (AMR)

AF:

0.236

AC:

AN:

106

Ashkenazi Jewish (ASJ)

AF:

0.227

AC:

AN:

154

East Asian (EAS)

AF:

0.396

AC:

259

AN:

654

South Asian (SAS)

AF:

0.205

AC:

AN:

European-Finnish (FIN)

AF:

0.201

AC:

136

AN:

676

Middle Eastern (MID)

AF:

0.192

AC:

AN:

European-Non Finnish (NFE)

AF:

0.187

AC:

580

AN:

3104

Other (OTH)

AF:

0.212

AC:

AN:

306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

125

166

208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.279

AC:

41612

AN:

149094

Hom.:

6203

Cov.:

AF XY:

0.278

AC XY:

20242

AN XY:

72782

show subpopulations

African (AFR)

AF:

0.392

AC:

15903

AN:

40582

American (AMR)

AF:

0.231

AC:

3474

AN:

15064

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1024

AN:

3458

East Asian (EAS)

AF:

0.417

AC:

2153

AN:

5160

South Asian (SAS)

AF:

0.268

AC:

1279

AN:

4778

European-Finnish (FIN)

AF:

0.266

AC:

2638

AN:

9910

Middle Eastern (MID)

AF:

0.176

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.215

AC:

14381

AN:

66896

Other (OTH)

AF:

0.282

AC:

587

AN:

2078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1529

3058

4586

6115

7644

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.242

Hom.:

15075

Bravo

AF:

0.276

Asia WGS

AF:

0.371

AC:

1285

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.7

(source)

DANN

Benign

0.42

PhyloP100

-0.032

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over