14-93246298-TAAAAA-TAAA

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
• 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: 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.

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.2122-14_2122-13delTT		intron	N/A	NP_001002860.2	Q9P203-1
	BTBD7	NM_001289133.2		c.1069-14_1069-13delTT		intron	N/A	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.2122-14_2122-13delTT		intron	N/A	ENSP00000335615.5	Q9P203-1
	BTBD7	ENST00000554565.5	TSL:1	c.1069-14_1069-13delTT		intron	N/A	ENSP00000451010.1	Q9P203-5
	BTBD7	ENST00000893710.1		c.2122-14_2122-13delTT		intron	N/A	ENSP00000563769.1

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

African (AFR) AF: 0.395 AC: 10533 AN: 26660

American (AMR) AF: 0.259 AC: 5544 AN: 21438

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 4463 AN: 17082

East Asian (EAS) AF: 0.317 AC: 10968 AN: 34568

South Asian (SAS) AF: 0.308 AC: 14207 AN: 46150

European-Finnish (FIN) AF: 0.241 AC: 9675 AN: 40086

Middle Eastern (MID) AF: 0.248 AC: 1156 AN: 4664

European-Non Finnish (NFE) AF: 0.236 AC: 225044 AN: 953472

Other (OTH) 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

African (AFR) AF: 0.451 AC: 17693 AN: 39258

American (AMR) AF: 0.258 AC: 3722 AN: 14428

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 948 AN: 3318

East Asian (EAS) AF: 0.302 AC: 1503 AN: 4978

South Asian (SAS) AF: 0.336 AC: 1532 AN: 4564

European-Finnish (FIN) AF: 0.254 AC: 2266 AN: 8924

Middle Eastern (MID) AF: 0.301 AC: 83 AN: 276

European-Non Finnish (NFE) AF: 0.253 AC: 16386 AN: 64738

Other (OTH) AF: 0.316 AC: 632 AN: 1998

Alfa AF: 0.136 Hom.: 84

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
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

Other links and lift over

dbSNP: rs55659625; hg19: chr14-93712644;