14-93242630-G-T

Variant names:

• chr14-93242630-G-T
• rs751931563
• NM_001002860.4:c.3042C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001002860.4(BTBD7):​c.3042C>A​(p.Asp1014Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BTBD7 NM_001002860.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -1.52
• Publications: 0 publications found

Genes affected

BTBD7 (HGNC:18269): (BTB domain containing 7) Predicted to be involved in regulation of branching involved in salivary gland morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.034065127).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002860.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD7	NM_001002860.4	MANE Select	c.3042C>A	p.Asp1014Glu	missense	Exon 11 of 11	NP_001002860.2	Q9P203-1
	BTBD7	NM_001289133.2		c.1989C>A	p.Asp663Glu	missense	Exon 9 of 9	NP_001276062.1	Q9P203-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTBD7	ENST00000334746.10	TSL:1 MANE Select	c.3042C>A	p.Asp1014Glu	missense	Exon 11 of 11	ENSP00000335615.5	Q9P203-1
	BTBD7	ENST00000554565.5	TSL:1	c.1989C>A	p.Asp663Glu	missense	Exon 9 of 9	ENSP00000451010.1	Q9P203-5
	BTBD7	ENST00000893710.1		c.3042C>A	p.Asp1014Glu	missense	Exon 12 of 12	ENSP00000563769.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.0050
DANN	Benign	0.89
DEOGEN2	Benign	0.013	T
Eigen	Benign	-2.2
Eigen_PC	Benign	-2.3
FATHMM_MKL	Benign	0.048	N
M_CAP	Benign	0.0079	T
MetaRNN	Benign	0.034	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.34	N
PhyloP100		-1.5
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-0.37	N
REVEL	Benign	0.077
Sift	Benign	0.077	T
Sift4G	Benign	0.51	T
Polyphen		0.0010	B
Vest4		0.090
MutPred		0.11		Loss of glycosylation at S1012 (P = 0.1491)
MVP		0.46
MPC		0.16
ClinPred		0.13	T
GERP RS		-12
Varity_R		0.057
gMVP		0.17
Mutation Taster		=85/15	polymorphism

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: rs751931563; hg19: chr14-93708976;