14-93246298-TAAAA-TA

Position:

• chr14-93246298-TAAAA-TA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001002860.4(BTBD7):​c.2122-15_2122-13delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 1,328,896 control chromosomes in the GnomAD database, including 99 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.015 (16 hom., cov: 0)
  • Exomes 𝑓: 0.032 (83 hom.)
• Consequence: BTBD7 NM_001002860.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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 Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD7	NM_001002860.4	c.2122-15_2122-13delTTT		intron_variant		ENST00000334746.10	NP_001002860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD7	ENST00000334746.10	c.2122-15_2122-13delTTT		intron_variant		1	NM_001002860.4	ENSP00000335615.5
BTBD7	ENST00000554565.5	c.1069-15_1069-13delTTT		intron_variant		1		ENSP00000451010.1
BTBD7	ENST00000553975.1	c.967-15_967-13delTTT		intron_variant		2		ENSP00000450778.1
BTBD7	ENST00000355125.3	n.*743-15_*743-13delTTT		intron_variant		2		ENSP00000347246.3

Frequencies

GnomAD3 genomes AF: 0.0146 AC: 2085 AN: 142564 Hom.: 16 Cov.: 0

Gnomad AFR AF: 0.00428

Gnomad AMI AF: 0.00228

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.0316

Gnomad EAS AF: 0.000405

Gnomad SAS AF: 0.0229

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0367

Gnomad NFE AF: 0.0221

Gnomad OTH AF: 0.0112

GnomAD3 exomes AF: 0.0457 AC: 4944 AN: 108090 Hom.: 17 AF XY: 0.0463 AC XY: 2709 AN XY: 58568

Gnomad AFR exome AF: 0.0699

Gnomad AMR exome AF: 0.0333

Gnomad ASJ exome AF: 0.0664

Gnomad EAS exome AF: 0.0294

Gnomad SAS exome AF: 0.0675

Gnomad FIN exome AF: 0.0280

Gnomad NFE exome AF: 0.0463

Gnomad OTH exome AF: 0.0528

GnomAD4 exome AF: 0.0321 AC: 38060 AN: 1186250 Hom.: 83 AF XY: 0.0329 AC XY: 18931 AN XY: 575406

Gnomad4 AFR exome AF: 0.0422

Gnomad4 AMR exome AF: 0.0263

Gnomad4 ASJ exome AF: 0.0444

Gnomad4 EAS exome AF: 0.0145

Gnomad4 SAS exome AF: 0.0597

Gnomad4 FIN exome AF: 0.0240

Gnomad4 NFE exome AF: 0.0311

Gnomad4 OTH exome AF: 0.0342

GnomAD4 genome AF: 0.0146 AC: 2088 AN: 142646 Hom.: 16 Cov.: 0 AF XY: 0.0141 AC XY: 979 AN XY: 69254

Gnomad4 AFR AF: 0.00432

Gnomad4 AMR AF: 0.0105

Gnomad4 ASJ AF: 0.0316

Gnomad4 EAS AF: 0.000406

Gnomad4 SAS AF: 0.0237

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.0221

Gnomad4 OTH AF: 0.0110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs55659625; hg19: chr14-93712644;