14-93246298-TAAAA-TAAAAA

Position:

• chr14-93246298-TAAAA-TAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000334746.10(BTBD7):​c.2122-13_2122-12insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00079 (0 hom., cov: 0)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: BTBD7 ENST00000334746.10 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD7	NM_001002860.4	c.2122-13_2122-12insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000334746.10	NP_001002860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD7	ENST00000334746.10	c.2122-13_2122-12insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001002860.4	ENSP00000335615	P1
BTBD7	ENST00000554565.5	c.1069-13_1069-12insT		splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000451010
BTBD7	ENST00000553975.1	c.967-13_967-12insT		splice_polypyrimidine_tract_variant, intron_variant		2		ENSP00000450778
BTBD7	ENST00000355125.3	c.*743-13_*743-12insT		splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		2		ENSP00000347246

Frequencies

GnomAD3 genomes AF: 0.000793 AC: 113 AN: 142550 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00343

Gnomad ASJ AF: 0.00485

Gnomad EAS AF: 0.000405

Gnomad SAS AF: 0.000883

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000372

Gnomad OTH AF: 0.000507

GnomAD3 exomes AF: 0.0110 AC: 1189 AN: 108090 Hom.: 0 AF XY: 0.0103 AC XY: 601 AN XY: 58568

Gnomad AFR exome AF: 0.00659

Gnomad AMR exome AF: 0.0117

Gnomad ASJ exome AF: 0.0136

Gnomad EAS exome AF: 0.0120

Gnomad SAS exome AF: 0.00943

Gnomad FIN exome AF: 0.00743

Gnomad NFE exome AF: 0.0121

Gnomad OTH exome AF: 0.0139

GnomAD4 exome AF: 0.0123 AC: 14710 AN: 1192188 Hom.: 0 Cov.: 0 AF XY: 0.0122 AC XY: 7043 AN XY: 578668

Gnomad4 AFR exome AF: 0.00576

Gnomad4 AMR exome AF: 0.00853

Gnomad4 ASJ exome AF: 0.0126

Gnomad4 EAS exome AF: 0.00558

Gnomad4 SAS exome AF: 0.0145

Gnomad4 FIN exome AF: 0.00793

Gnomad4 NFE exome AF: 0.0130

Gnomad4 OTH exome AF: 0.0113

GnomAD4 genome AF: 0.000792 AC: 113 AN: 142632 Hom.: 0 Cov.: 0 AF XY: 0.000924 AC XY: 64 AN XY: 69242

Gnomad4 AFR AF: 0.000204

Gnomad4 AMR AF: 0.00343

Gnomad4 ASJ AF: 0.00485

Gnomad4 EAS AF: 0.000406

Gnomad4 SAS AF: 0.000663

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.000372

Gnomad4 OTH AF: 0.000502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs55659625; hg19: chr14-93712644;