10-122286372-A-G

Variant names:

• chr10-122286372-A-G
• rs911774
• NM_144587.5:c.385+124A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144587.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD16	NM_144587.5	MANE Select	c.385+124A>G		intron	N/A	NP_653188.2
	BTBD16	NM_001318189.3		c.388+124A>G		intron	N/A	NP_001305118.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD16	ENST00000260723.6	TSL:2 MANE Select	c.385+124A>G		intron	N/A	ENSP00000260723.4

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

African (AFR) AF: 0.944 AC: 25816 AN: 27350

American (AMR) AF: 0.876 AC: 20760 AN: 23710

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 14895 AN: 18064

East Asian (EAS) AF: 1.00 AC: 36287 AN: 36300

South Asian (SAS) AF: 0.931 AC: 51438 AN: 55262

European-Finnish (FIN) AF: 0.807 AC: 27277 AN: 33780

Middle Eastern (MID) AF: 0.872 AC: 3050 AN: 3496

European-Non Finnish (NFE) AF: 0.792 AC: 761232 AN: 961634

Other (OTH) AF: 0.832 AC: 41994 AN: 50500

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

African (AFR) AF: 0.938 AC: 38952 AN: 41542

American (AMR) AF: 0.844 AC: 12912 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2822 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5176

South Asian (SAS) AF: 0.944 AC: 4552 AN: 4820

European-Finnish (FIN) AF: 0.798 AC: 8458 AN: 10598

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53582 AN: 68008

Other (OTH) AF: 0.831 AC: 1753 AN: 2110

Alfa AF: 0.814 Hom.: 55902

Bravo AF: 0.858

Asia WGS AF: 0.969 AC: 3368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.35
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs911774; hg19: chr10-124045887;