14-93246298-TAAAA-TAA

Variant names:

• chr14-93246298-TAA-T
• rs55659625
• NM_001002860.4:c.2122-14_2122-13delTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001002860.4(BTBD7):​c.2122-14_2122-13delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,336,614 control chromosomes in the GnomAD database, including 10,800 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (5439 hom., cov: 0)
  • Exomes 𝑓: 0.25 (5361 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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD7	NM_001002860.4	c.2122-14_2122-13delTT		intron_variant	Intron 9 of 10	ENST00000334746.10	NP_001002860.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD7	ENST00000334746.10	c.2122-14_2122-13delTT		intron_variant	Intron 9 of 10	1	NM_001002860.4	ENSP00000335615.5
BTBD7	ENST00000554565.5	c.1069-14_1069-13delTT		intron_variant	Intron 7 of 8	1		ENSP00000451010.1
BTBD7	ENST00000553975.1	c.967-14_967-13delTT		intron_variant	Intron 5 of 6	2		ENSP00000450778.1
BTBD7	ENST00000355125.3	n.*743-14_*743-13delTT		intron_variant	Intron 6 of 7	2		ENSP00000347246.3

Frequencies

GnomAD3 genomes AF: 0.314 AC: 44943 AN: 143282 Hom.: 5427 Cov.: 0

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.313

GnomAD2 exomes AF: 0.285 AC: 30854 AN: 108090 AF XY: 0.283

Gnomad AFR exome AF: 0.416

Gnomad AMR exome AF: 0.265

Gnomad ASJ exome AF: 0.302

Gnomad EAS exome AF: 0.317

Gnomad FIN exome AF: 0.257

Gnomad NFE exome AF: 0.262

Gnomad OTH exome AF: 0.284

GnomAD4 exome AF: 0.247 AC: 294245 AN: 1193252 Hom.: 5361 AF XY: 0.247 AC XY: 143182 AN XY: 578980

Gnomad4 AFR exome AF: 0.395 AC: 10533 AN: 26660

Gnomad4 AMR exome AF: 0.259 AC: 5544 AN: 21438

Gnomad4 ASJ exome AF: 0.261 AC: 4463 AN: 17082

Gnomad4 EAS exome AF: 0.317 AC: 10968 AN: 34568

Gnomad4 SAS exome AF: 0.308 AC: 14207 AN: 46150

Gnomad4 FIN exome AF: 0.241 AC: 9675 AN: 40086

Gnomad4 NFE exome AF: 0.236 AC: 225044 AN: 953472

Gnomad4 Remaining exome AF: 0.258 AC: 12655 AN: 49132

GnomAD4 genome AF: 0.314 AC: 45004 AN: 143362 Hom.: 5439 Cov.: 0 AF XY: 0.312 AC XY: 21731 AN XY: 69618

Gnomad4 AFR AF: 0.451 AC: 0.450685 AN: 0.450685

Gnomad4 AMR AF: 0.258 AC: 0.257971 AN: 0.257971

Gnomad4 ASJ AF: 0.286 AC: 0.285714 AN: 0.285714

Gnomad4 EAS AF: 0.302 AC: 0.301928 AN: 0.301928

Gnomad4 SAS AF: 0.336 AC: 0.33567 AN: 0.33567

Gnomad4 FIN AF: 0.254 AC: 0.253922 AN: 0.253922

Gnomad4 NFE AF: 0.253 AC: 0.253113 AN: 0.253113

Gnomad4 OTH AF: 0.316 AC: 0.316316 AN: 0.316316

Alfa AF: 0.136 Hom.: 84

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=100/0	polymorphism (auto)

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;