14-93246298-TAAAAA-T

Variant names:

• chr14-93246298-TAAAAA-T
• rs55659625
• NM_001002860.4:c.2122-17_2122-13delTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001002860.4(BTBD7):​c.2122-17_2122-13delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,208,008 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000025 (0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.2122-17_2122-13delTTTTT		intron	N/A	NP_001002860.2	Q9P203-1
	BTBD7	NM_001289133.2		c.1069-17_1069-13delTTTTT		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.2122-17_2122-13delTTTTT		intron	N/A	ENSP00000335615.5	Q9P203-1
	BTBD7	ENST00000554565.5	TSL:1	c.1069-17_1069-13delTTTTT		intron	N/A	ENSP00000451010.1	Q9P203-5
	BTBD7	ENST00000893710.1		c.2122-17_2122-13delTTTTT		intron	N/A	ENSP00000563769.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000248 AC: 3 AN: 1208008 Hom.: 0 AF XY: 0.00000171 AC XY: 1 AN XY: 586114

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

African (AFR) AF: 0.00 AC: 0 AN: 26874

American (AMR) AF: 0.00 AC: 0 AN: 21682

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17266

East Asian (EAS) AF: 0.00 AC: 0 AN: 34892

South Asian (SAS) AF: 0.0000214 AC: 1 AN: 46738

European-Finnish (FIN) AF: 0.0000247 AC: 1 AN: 40500

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4704

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 965728

Other (OTH) AF: 0.0000202 AC: 1 AN: 49624

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000178044), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs55659625; hg19: chr14-93712644;