10-122329210-C-T

Position:

• chr10-122329210-C-T

Variant summary

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

The NM_144587.5(BTBD16):​c.912-270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 152,026 control chromosomes in the GnomAD database, including 24,358 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 0.56 (24358 hom., cov: 32)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD16	NM_144587.5	c.912-270C>T		intron_variant		ENST00000260723.6	NP_653188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD16	ENST00000260723.6	c.912-270C>T		intron_variant		2	NM_144587.5	ENSP00000260723.4

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85226 AN: 151908 Hom.: 24324 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.561 AC: 85306 AN: 152026 Hom.: 24358 Cov.: 32 AF XY: 0.567 AC XY: 42140 AN XY: 74330

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.551

Alfa AF: 0.531 Hom.: 2718

Bravo AF: 0.569

Asia WGS AF: 0.688 AC: 2391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.066
DANN	Benign	0.57

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: rs927427; hg19: chr10-124088725;