rs7078071

Variant names:

• chr10-122278557-G-A
• rs7078071
• NM_144587.5:c.167+1618G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-122278557-G-A
• chr10-122278557-G-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.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
• Publications: 5 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 = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD16	NM_144587.5	c.167+1618G>A		intron_variant	Intron 3 of 15	ENST00000260723.6	NP_653188.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD16	ENST00000260723.6	c.167+1618G>A		intron_variant	Intron 3 of 15	2	NM_144587.5	ENSP00000260723.4

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

African (AFR) AF: 0.166 AC: 6881 AN: 41502

American (AMR) AF: 0.0510 AC: 780 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0502 AC: 174 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0199 AC: 96 AN: 4820

European-Finnish (FIN) AF: 0.0431 AC: 457 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0602 AC: 4092 AN: 67990

Other (OTH) AF: 0.0730 AC: 154 AN: 2110

Alfa AF: 0.0386 Hom.: 49

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
PhyloP100		-0.68
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: rs7078071; hg19: chr10-124038072;