rs7893461

Variant names:

• chr10-122276179-G-T
• rs7893461
• NM_144587.5:c.19-612G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144587.5(BTBD16):​c.19-612G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,240 control chromosomes in the GnomAD database, including 1,967 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 0.12 (1967 hom., cov: 33)
• Consequence: BTBD16 NM_144587.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD16	NM_144587.5	c.19-612G>T		intron_variant	Intron 2 of 15	ENST00000260723.6	NP_653188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD16	ENST00000260723.6	c.19-612G>T		intron_variant	Intron 2 of 15	2	NM_144587.5	ENSP00000260723.4

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18240 AN: 152122 Hom.: 1965 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0430

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.120 AC: 18255 AN: 152240 Hom.: 1967 Cov.: 33 AF XY: 0.114 AC XY: 8505 AN XY: 74452

African (AFR) AF: 0.294 AC: 12186 AN: 41506

American (AMR) AF: 0.0625 AC: 957 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4834

European-Finnish (FIN) AF: 0.0430 AC: 456 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4110 AN: 68008

Other (OTH) AF: 0.105 AC: 222 AN: 2116

Alfa AF: 0.0765 Hom.: 1227

Bravo AF: 0.132

Asia WGS AF: 0.0250 AC: 89 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	0.56
DANN	Benign	0.60
PhyloP100		-0.73
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: rs7893461; hg19: chr10-124035694; COSMIC: COSV53261172;