chr10-122286372-A-G

Position:

• chr10-122286372-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.385+124A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 1,362,322 control chromosomes in the GnomAD database, including 455,716 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 0.85 (55190 hom., cov: 32)
  • Exomes 𝑓: 0.81 (400526 hom.)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD16	NM_144587.5	c.385+124A>G		intron_variant		ENST00000260723.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD16	ENST00000260723.6	c.385+124A>G		intron_variant		2	NM_144587.5	P1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129014 AN: 152108 Hom.: 55129 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.829

GnomAD4 exome AF: 0.812 AC: 982749 AN: 1210096 Hom.: 400526 AF XY: 0.815 AC XY: 481038 AN XY: 590414

Gnomad4 AFR exome AF: 0.944

Gnomad4 AMR exome AF: 0.876

Gnomad4 ASJ exome AF: 0.825

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.931

Gnomad4 FIN exome AF: 0.807

Gnomad4 NFE exome AF: 0.792

Gnomad4 OTH exome AF: 0.832

GnomAD4 genome AF: 0.848 AC: 129133 AN: 152226 Hom.: 55190 Cov.: 32 AF XY: 0.850 AC XY: 63247 AN XY: 74420

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.831

Alfa AF: 0.813 Hom.: 34645

Bravo AF: 0.858

Asia WGS AF: 0.969 AC: 3368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs911774; hg19: chr10-124045887;