10-122336791-T-C

Variant names:

• chr10-122336791-T-C
• rs3817285
• NM_144587.5:c.1452+109T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144587.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD16	NM_144587.5	MANE Select	c.1452+109T>C		intron	N/A	NP_653188.2	Q32M84-1
	BTBD16	NM_001318189.3		c.1455+109T>C		intron	N/A	NP_001305118.1	Q32M84-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD16	ENST00000260723.6	TSL:2 MANE Select	c.1452+109T>C		intron	N/A	ENSP00000260723.4	Q32M84-1
	BTBD16	ENST00000495370.2	TSL:3	n.*169T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94319 AN: 151896 Hom.: 29903 Cov.: 32

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

African (AFR) AF: 0.645 AC: 10983 AN: 17018

American (AMR) AF: 0.722 AC: 9058 AN: 12546

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 7482 AN: 15178

East Asian (EAS) AF: 0.968 AC: 26480 AN: 27354

South Asian (SAS) AF: 0.640 AC: 23649 AN: 36936

European-Finnish (FIN) AF: 0.618 AC: 20915 AN: 33870

Middle Eastern (MID) AF: 0.612 AC: 2506 AN: 4098

European-Non Finnish (NFE) AF: 0.538 AC: 320320 AN: 595496

Other (OTH) AF: 0.596 AC: 21727 AN: 36444

GnomAD4 genome AF: 0.621 AC: 94423 AN: 152014 Hom.: 29953 Cov.: 32 AF XY: 0.630 AC XY: 46800 AN XY: 74308

African (AFR) AF: 0.666 AC: 27585 AN: 41438

American (AMR) AF: 0.707 AC: 10820 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3472

East Asian (EAS) AF: 0.961 AC: 4969 AN: 5172

South Asian (SAS) AF: 0.680 AC: 3276 AN: 4818

European-Finnish (FIN) AF: 0.623 AC: 6580 AN: 10558

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37539 AN: 67942

Other (OTH) AF: 0.609 AC: 1288 AN: 2114

Alfa AF: 0.550 Hom.: 12327

Bravo AF: 0.634

Asia WGS AF: 0.824 AC: 2866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.91
DANN	Benign	0.45
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3817285; hg19: chr10-124096306;