10-122297259-A-G

Position:

• chr10-122297259-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.591-509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 152,112 control chromosomes in the GnomAD database, including 25,343 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 (25343 hom., cov: 33)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD16	NM_144587.5	c.591-509A>G		intron_variant		ENST00000260723.6	NP_653188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD16	ENST00000260723.6	c.591-509A>G		intron_variant		2	NM_144587.5	ENSP00000260723.4

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85638 AN: 151996 Hom.: 25281 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.564 AC: 85754 AN: 152112 Hom.: 25343 Cov.: 33 AF XY: 0.571 AC XY: 42504 AN XY: 74376

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.538

Alfa AF: 0.495 Hom.: 9697

Bravo AF: 0.574

Asia WGS AF: 0.766 AC: 2664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.38

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: rs7907952; hg19: chr10-124056774; COSMIC: COSV53264243;