chr10-122285159-A-G

Position:

• chr10-122285159-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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/exons	MANE	UniProt
BTBD16	NM_144587.5	c.242-946A>G		intron_variant		ENST00000260723.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD16	ENST00000260723.6	c.242-946A>G		intron_variant		2	NM_144587.5	P1

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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.458

Alfa AF: 0.465 Hom.: 7891

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

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: rs1028631; hg19: chr10-124044674;