10-122285159-A-G

Variant names:

• chr10-122285159-A-G
• rs1028631
• NM_144587.5:c.242-946A>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.242-946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,770 control chromosomes in the GnomAD database, including 17,224 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 0.46 (17224 hom., cov: 31)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD16	NM_144587.5	c.242-946A>G		intron_variant	Intron 4 of 15	ENST00000260723.6	NP_653188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD16	ENST00000260723.6	c.242-946A>G		intron_variant	Intron 4 of 15	2	NM_144587.5	ENSP00000260723.4

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69555 AN: 151652 Hom.: 17206 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.459 AC: 69606 AN: 151770 Hom.: 17224 Cov.: 31 AF XY: 0.469 AC XY: 34790 AN XY: 74178

African (AFR) AF: 0.315 AC: 13030 AN: 41356

American (AMR) AF: 0.566 AC: 8633 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1554 AN: 3464

East Asian (EAS) AF: 0.892 AC: 4595 AN: 5150

South Asian (SAS) AF: 0.566 AC: 2718 AN: 4798

European-Finnish (FIN) AF: 0.557 AC: 5878 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31639 AN: 67886

Other (OTH) AF: 0.458 AC: 966 AN: 2108

Alfa AF: 0.464 Hom.: 8713

Bravo AF: 0.455

Asia WGS AF: 0.736 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.29
DANN	Benign	0.33
PhyloP100		-0.88
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: rs1028631; hg19: chr10-124044674;