Genetic Variant NM_001002860.4:c.2122-17_2122-13delTTTTT (chr14-93246298-TAAAAA-T) – ACMG Classification: Uncertain_significance (2 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08

Publications

0 publications found

Variant links:

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]

BTBD7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTBD7	NM_001002860.4 link	c.2122-17_2122-13delTTTTT		intron_variant	Intron 9 of 10	ENST00000334746.10	NP_001002860.2	Q9P203-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BTBD7	ENST00000334746.10 link	c.2122-17_2122-13delTTTTT	intron_variant	Intron 9 of 10	1	NM_001002860.4	ENSP00000335615.5	Q9P203-1
BTBD7	ENST00000554565.5 link	c.1069-17_1069-13delTTTTT	intron_variant	Intron 7 of 8	1		ENSP00000451010.1	Q9P203-5
BTBD7	ENST00000553975.1 link	c.967-17_967-13delTTTTT	intron_variant	Intron 5 of 6	2		ENSP00000450778.1	H0YJ41
BTBD7	ENST00000355125.3 link	n.743-17_743-13delTTTTT	intron_variant	Intron 6 of 7	2		ENSP00000347246.3	H3BLV3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000248

AC:

AN:

1208008

Hom.:

AF XY:

0.00000171

AC XY:

AN XY:

586114

show subpopulations

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

African (AFR)

AF:

0.00

AC:

AN:

26874

American (AMR)

AF:

0.00

AC:

AN:

21682

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17266

East Asian (EAS)

AF:

0.00

AC:

AN:

34892

South Asian (SAS)

AF:

0.0000214

AC:

AN:

46738

European-Finnish (FIN)

AF:

0.0000247

AC:

AN:

40500

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4704

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

965728

Other (OTH)

AF:

0.0000202

AC:

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.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over