Genetic Variant ENST00000611838.1:n.131+67T>C (chr6-32255481-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000611838.1(TSBP1-AS1):n.131+67T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 154,388 control chromosomes in the GnomAD database, including 36,478 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 0.68 ( 35791 hom., cov: 32)

Exomes 𝑓: 0.76 ( 687 hom. )

Consequence

TSBP1-AS1
ENST00000611838.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

70 publications found

Variant links:

Genes affected

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

TSBP1-AS1 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TSBP1-AS1	NR_136244.1 link	n.242+67T>C	intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136245.1 link	n.242+67T>C	intron_variant	Intron 1 of 3
TSBP1-AS1	NR_136246.1 link	n.242+67T>C	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TSBP1-AS1	ENST00000611838.1 link	n.131+67T>C	intron_variant	Intron 1 of 1	2
TSBP1-AS1	ENST00000644884.2 link	n.64+67T>C	intron_variant	Intron 1 of 3
TSBP1-AS1	ENST00000645134.1 link	n.87+67T>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103716

AN:

151968

Hom.:

35759

Cov.:

show subpopulations

Gnomad AFR

AF:

0.711

Gnomad AMI

AF:

0.663

Gnomad AMR

AF:

0.779

Gnomad ASJ

AF:

0.858

Gnomad EAS

AF:

0.773

Gnomad SAS

AF:

0.758

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.835

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.715

GnomAD4 exome

AF:

0.762

AC:

1753

AN:

2302

Hom.:

687

Cov.:

AF XY:

0.780

AC XY:

1012

AN XY:

1298

show subpopulations

African (AFR)

AF:

0.944

AC:

AN:

American (AMR)

AF:

0.868

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.875

AC:

AN:

East Asian (EAS)

AF:

0.967

AC:

AN:

South Asian (SAS)

AF:

0.896

AC:

346

AN:

386

European-Finnish (FIN)

AF:

0.627

AC:

AN:

118

Middle Eastern (MID)

AF:

0.833

AC:

AN:

European-Non Finnish (NFE)

AF:

0.720

AC:

1076

AN:

1494

Other (OTH)

AF:

0.778

AC:

AN:

126

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.545

Heterozygous variant carriers

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:

0.683

AC:

103804

AN:

152086

Hom.:

35791

Cov.:

AF XY:

0.683

AC XY:

50790

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.711

AC:

29512

AN:

41504

American (AMR)

AF:

0.779

AC:

11899

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.858

AC:

2974

AN:

3468

East Asian (EAS)

AF:

0.773

AC:

3992

AN:

5166

South Asian (SAS)

AF:

0.759

AC:

3658

AN:

4818

European-Finnish (FIN)

AF:

0.574

AC:

6068

AN:

10574

Middle Eastern (MID)

AF:

0.830

AC:

244

AN:

294

European-Non Finnish (NFE)

AF:

0.638

AC:

43341

AN:

67962

Other (OTH)

AF:

0.714

AC:

1511

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1673

3346

5018

6691

8364

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.660

Hom.:

116347

Bravo

AF:

0.699

Asia WGS

AF:

0.746

AC:

2596

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.2

(source)

DANN

Benign

0.78

PhyloP100

-0.031

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