Genetic Variant BTBD16:c.1452+109T>C (chr10-122336791-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_144587.5(BTBD16):c.1452+109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 930,954 control chromosomes in the GnomAD database, including 159,826 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 0.62 ( 29953 hom., cov: 32)

Exomes 𝑓: 0.57 ( 129873 hom. )

Consequence

BTBD16
NM_144587.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Variant links:

Genes affected

BTBD16 (HGNC:26340): (BTB domain containing 16) This gene encodes a protein that contains a BTB/POZ domain. This domain mediates protein-protein interactions. A mutation in this gene may be associated with bipolar disorder. [provided by RefSeq, Sep 2016]

BTBD16 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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD16	NM_144587.5 link	c.1452+109T>C		intron_variant	Intron 15 of 15	ENST00000260723.6	NP_653188.2	Q32M84-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD16	ENST00000260723.6 link	c.1452+109T>C		intron_variant	Intron 15 of 15	2	NM_144587.5	ENSP00000260723.4		Q32M84-1
BTBD16	ENST00000495370.2 link	n.*169T>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

94319

AN:

151896

Hom.:

29903

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.707

Gnomad ASJ

AF:

0.489

Gnomad EAS

AF:

0.961

Gnomad SAS

AF:

0.680

Gnomad FIN

AF:

0.623

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.553

Gnomad OTH

AF:

0.605

GnomAD4 exome

AF:

0.569

AC:

443120

AN:

778940

Hom.:

129873

AF XY:

0.570

AC XY:

220203

AN XY:

386544

show subpopulations

Gnomad4 AFR exome

AF:

0.645

Gnomad4 AMR exome

AF:

0.722

Gnomad4 ASJ exome

AF:

0.493

Gnomad4 EAS exome

AF:

0.968

Gnomad4 SAS exome

AF:

0.640

Gnomad4 FIN exome

AF:

0.618

Gnomad4 NFE exome

AF:

0.538

Gnomad4 OTH exome

AF:

0.596

GnomAD4 genome

AF:

0.621

AC:

94423

AN:

152014

Hom.:

29953

Cov.:

AF XY:

0.630

AC XY:

46800

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.666

Gnomad4 AMR

AF:

0.707

Gnomad4 ASJ

AF:

0.489

Gnomad4 EAS

AF:

0.961

Gnomad4 SAS

AF:

0.680

Gnomad4 FIN

AF:

0.623

Gnomad4 NFE

AF:

0.553

Gnomad4 OTH

AF:

0.609

Alfa

AF:

0.549

Hom.:

10947

Bravo

AF:

0.634

Asia WGS

AF:

0.824

AC:

2866

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.91

DANN

Benign

0.45

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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.

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