rs7893461

chr10-122276179-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144587.5(BTBD16):c.19-612G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,240 control chromosomes in the GnomAD database, including 1,967 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 0.12 (1967 hom., cov: 33)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD16	NM_144587.5	c.19-612G>T		intron_variant		ENST00000260723.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD16	ENST00000260723.6	c.19-612G>T		intron_variant		2	NM_144587.5	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18240 AN: 152122 Hom.: 1965 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.120 AC: 18255 AN: 152240 Hom.: 1967 Cov.: 33 AF XY: 0.114 AC XY: 8505 AN XY: 74452

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.0625

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.0430

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0685 Hom.: 724

Bravo AF: 0.132

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.56
Dann	Benign	0.60

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

Publications

LitVar

Other links and lift over

dbSNP: rs7893461; hg19: chr10-124035694; COSMIC: COSV53261172;