Variant 6-32377506-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_136244.1(TSBP1-AS1):n.501-5458C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,102 control chromosomes in the GnomAD database, including 145 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 0.041 ( 145 hom., cov: 32)

Consequence

TSBP1-AS1
NR_136244.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987

Variant links:

Genes affected

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

TSBP1-AS1 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSBP1-AS1	NR_136244.1 link	n.501-5458C>A		intron_variant
TSBP1-AS1	NR_136245.1 link	n.302+11667C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
TSBP1-AS1	ENST00000642577.1 link	n.168+11667C>A	intron_variant
TSBP1-AS1	ENST00000644884.2 link	n.125-9475C>A	intron_variant
TSBP1-AS1	ENST00000645134.1 link	n.88-12708C>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0415

AC:

6303

AN:

151984

Hom.:

145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0563

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0545

Gnomad ASJ

AF:

0.00606

Gnomad EAS

AF:

0.0270

Gnomad SAS

AF:

0.0496

Gnomad FIN

AF:

0.0657

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0284

Gnomad OTH

AF:

0.0469

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0415

AC:

6306

AN:

152102

Hom.:

145

Cov.:

AF XY:

0.0427

AC XY:

3175

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.0565

Gnomad4 AMR

AF:

0.0543

Gnomad4 ASJ

AF:

0.00606

Gnomad4 EAS

AF:

0.0269

Gnomad4 SAS

AF:

0.0486

Gnomad4 FIN

AF:

0.0657

Gnomad4 NFE

AF:

0.0284

Gnomad4 OTH

AF:

0.0464

Alfa

AF:

0.0253

Hom.:

Bravo

AF:

0.0414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.0

DANN

Benign

0.74

Splicing

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