10-122281932-A-G

Variant names:

• chr10-122281932-A-G
• rs6585810
• NM_144587.5:c.168-1919A>G

Variant summary

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

The NM_144587.5(BTBD16):​c.168-1919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,150 control chromosomes in the GnomAD database, including 33,171 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 0.65 (33171 hom., cov: 33)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 9 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 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.168-1919A>G		intron	N/A	NP_653188.2	Q32M84-1
	BTBD16	NM_001318189.3		c.171-1919A>G		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.168-1919A>G		intron	N/A	ENSP00000260723.4	Q32M84-1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98071 AN: 152032 Hom.: 33117 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.645 AC: 98181 AN: 152150 Hom.: 33171 Cov.: 33 AF XY: 0.648 AC XY: 48163 AN XY: 74370

African (AFR) AF: 0.835 AC: 34680 AN: 41514

American (AMR) AF: 0.665 AC: 10166 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1733 AN: 3466

East Asian (EAS) AF: 0.893 AC: 4615 AN: 5170

South Asian (SAS) AF: 0.589 AC: 2840 AN: 4818

European-Finnish (FIN) AF: 0.600 AC: 6350 AN: 10576

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35868 AN: 67992

Other (OTH) AF: 0.608 AC: 1284 AN: 2112

Alfa AF: 0.557 Hom.: 39649

Bravo AF: 0.664

Asia WGS AF: 0.774 AC: 2690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.82
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6585810; hg19: chr10-124041447;