rs61740740

Variant names:

• chr14-93242565-C-A
• rs61740740
• NM_001002860.4:c.3107G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-93242565-C-A
• chr14-93242565-C-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001002860.4(BTBD7):​c.3107G>T​(p.Arg1036Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000507 in 1,614,182 control chromosomes in the GnomAD database, including 3 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1036Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0028 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00027 (2 hom.)
• Consequence: BTBD7 NM_001002860.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.64
• Publications: 6 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: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0070793033).
• BS2: High Homozygotes in GnomAdExome4 at 2 gene

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.3107G>T	p.Arg1036Leu	missense	Exon 11 of 11	NP_001002860.2	Q9P203-1
	BTBD7	NM_001289133.2		c.2054G>T	p.Arg685Leu	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.3107G>T	p.Arg1036Leu	missense	Exon 11 of 11	ENSP00000335615.5	Q9P203-1
	BTBD7	ENST00000554565.5	TSL:1	c.2054G>T	p.Arg685Leu	missense	Exon 9 of 9	ENSP00000451010.1	Q9P203-5
	BTBD7	ENST00000893710.1		c.3107G>T	p.Arg1036Leu	missense	Exon 12 of 12	ENSP00000563769.1

Frequencies

GnomAD3 genomes AF: 0.00279 AC: 424 AN: 152170 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00985

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00191

GnomAD2 exomes AF: 0.000604 AC: 152 AN: 251448 AF XY: 0.000405

Gnomad AFR exome AF: 0.00844

Gnomad AMR exome AF: 0.000376

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000271 AC: 396 AN: 1461894 Hom.: 2 Cov.: 32 AF XY: 0.000212 AC XY: 154 AN XY: 727248

African (AFR) AF: 0.0105 AC: 353 AN: 33480

American (AMR) AF: 0.000447 AC: 20 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1112012

Other (OTH) AF: 0.000348 AC: 21 AN: 60396

GnomAD4 genome AF: 0.00278 AC: 423 AN: 152288 Hom.: 1 Cov.: 32 AF XY: 0.00274 AC XY: 204 AN XY: 74454

African (AFR) AF: 0.00979 AC: 407 AN: 41556

American (AMR) AF: 0.000588 AC: 9 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68034

Other (OTH) AF: 0.00189 AC: 4 AN: 2114

Alfa AF: 0.000721 Hom.: 2

Bravo AF: 0.00306

ESP6500AA AF: 0.00817 AC: 36

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000733 AC: 89

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.017	T
BayesDel_noAF	Pathogenic	0.21
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.025	T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Benign	0.079	D
MetaRNN	Benign	0.0071	T
MetaSVM	Benign	-0.45	T
MutationAssessor	Benign	0.97	L
PhyloP100		5.6
PrimateAI	Benign	0.46	T
PROVEAN	Benign	-1.3	N
REVEL	Uncertain	0.31
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.51
MVP		0.78
MPC		0.78
ClinPred		0.076	T
GERP RS		6.0
Varity_R		0.35
gMVP		0.57
Mutation Taster		=48/52	disease causing

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: rs61740740; hg19: chr14-93708911; COSMIC: COSV58288334; COSMIC: COSV58288334;