14-93246298-TAAAA-TAA

Variant summary

Our verdict is Benign. Variant got -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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
BTBD7NM_001002860.4 linkuse as main transcriptc.2122-14_2122-13delTT intron_variant ENST00000334746.10 NP_001002860.2 Q9P203-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BTBD7ENST00000334746.10 linkuse as main transcriptc.2122-14_2122-13delTT intron_variant 1 NM_001002860.4 ENSP00000335615.5 Q9P203-1
BTBD7ENST00000554565.5 linkuse as main transcriptc.1069-14_1069-13delTT intron_variant 1 ENSP00000451010.1 Q9P203-5
BTBD7ENST00000553975.1 linkuse as main transcriptc.967-14_967-13delTT intron_variant 2 ENSP00000450778.1 H0YJ41
BTBD7ENST00000355125.3 linkuse as main transcriptn.*743-14_*743-13delTT intron_variant 2 ENSP00000347246.3 H3BLV3

Frequencies

GnomAD3 genomes
AF:
0.314
AC:
44943
AN:
143282
Hom.:
5427
Cov.:
0
show subpopulations
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
GnomAD3 exomes
AF:
0.285
AC:
30854
AN:
108090
Hom.:
1049
AF XY:
0.283
AC XY:
16593
AN XY:
58568
show subpopulations
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 SAS exome
AF:
0.320
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
show subpopulations
Gnomad4 AFR exome
AF:
0.395
Gnomad4 AMR exome
AF:
0.259
Gnomad4 ASJ exome
AF:
0.261
Gnomad4 EAS exome
AF:
0.317
Gnomad4 SAS exome
AF:
0.308
Gnomad4 FIN exome
AF:
0.241
Gnomad4 NFE exome
AF:
0.236
Gnomad4 OTH exome
AF:
0.258
GnomAD4 genome
AF:
0.314
AC:
45004
AN:
143362
Hom.:
5439
Cov.:
0
AF XY:
0.312
AC XY:
21731
AN XY:
69618
show subpopulations
Gnomad4 AFR
AF:
0.451
Gnomad4 AMR
AF:
0.258
Gnomad4 ASJ
AF:
0.286
Gnomad4 EAS
AF:
0.302
Gnomad4 SAS
AF:
0.336
Gnomad4 FIN
AF:
0.254
Gnomad4 NFE
AF:
0.253
Gnomad4 OTH
AF:
0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs55659625; hg19: chr14-93712644; API