rs7078071

chr10-122278557-G-Achr10-122278557-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144587.5(BTBD16):c.167+1618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 152,152 control chromosomes in the GnomAD database, including 766 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 0.083 (766 hom., cov: 32)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD16	NM_144587.5	c.167+1618G>A		intron_variant		ENST00000260723.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD16	ENST00000260723.6	c.167+1618G>A		intron_variant		2	NM_144587.5	P1

Frequencies

GnomAD3 genomes AF: 0.0834 AC: 12674 AN: 152034 Hom.: 766 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0199

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0834 AC: 12682 AN: 152152 Hom.: 766 Cov.: 32 AF XY: 0.0790 AC XY: 5881 AN XY: 74398

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.0502

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0199

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.0730

Alfa AF: 0.0331 Hom.: 39

Bravo AF: 0.0908

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.37
Dann	Benign	0.47

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: rs7078071; hg19: chr10-124038072;