NM_001002860.4:c.2122-13delT

Variant names:

• chr14-93246298-TA-T
• rs55659625
• NM_001002860.4:c.2122-13delT

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001002860.4(BTBD7):​c.2122-13delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (108 hom., cov: 0)
  • Exomes 𝑓: 0.24 (18 hom.)
  • Failed GnomAD Quality Control
• Consequence: BTBD7 NM_001002860.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.796
• 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: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 14-93246298-TA-T is Benign according to our data. Variant chr14-93246298-TA-T is described in ClinVar as Benign. ClinVar VariationId is 402435.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 108 gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 24022 AN: 138108 Hom.: 107 Cov.: 0

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.163

GnomAD2 exomes AF: 0.272 AC: 29394 AN: 108090 AF XY: 0.274

Gnomad AFR exome AF: 0.211

Gnomad AMR exome AF: 0.318

Gnomad ASJ exome AF: 0.220

Gnomad EAS exome AF: 0.290

Gnomad FIN exome AF: 0.297

Gnomad NFE exome AF: 0.272

Gnomad OTH exome AF: 0.257

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.239 AC: 263344 AN: 1103622 Hom.: 18 Cov.: 0 AF XY: 0.237 AC XY: 127078 AN XY: 535736

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.190 AC: 4752 AN: 24976

American (AMR) AF: 0.269 AC: 5467 AN: 20342

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 2991 AN: 15324

East Asian (EAS) AF: 0.226 AC: 7101 AN: 31410

South Asian (SAS) AF: 0.203 AC: 9107 AN: 44792

European-Finnish (FIN) AF: 0.230 AC: 8477 AN: 36890

Middle Eastern (MID) AF: 0.233 AC: 1010 AN: 4344

European-Non Finnish (NFE) AF: 0.243 AC: 214071 AN: 880460

Other (OTH) AF: 0.230 AC: 10368 AN: 45084

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.174 AC: 24045 AN: 138192 Hom.: 108 Cov.: 0 AF XY: 0.179 AC XY: 12037 AN XY: 67138

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.166 AC: 6339 AN: 38156

American (AMR) AF: 0.239 AC: 3303 AN: 13828

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 428 AN: 3184

East Asian (EAS) AF: 0.270 AC: 1274 AN: 4718

South Asian (SAS) AF: 0.185 AC: 815 AN: 4394

European-Finnish (FIN) AF: 0.199 AC: 1719 AN: 8632

Middle Eastern (MID) AF: 0.122 AC: 33 AN: 270

European-Non Finnish (NFE) AF: 0.155 AC: 9658 AN: 62242

Other (OTH) AF: 0.165 AC: 317 AN: 1926

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.114 Hom.: 84

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.80
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; COSMIC: COSV58285913; COSMIC: COSV58285913;