rs730414

chr11-13437307-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032320.7(BTBD10):c.101+7717G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,022 control chromosomes in the GnomAD database, including 29,990 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29990 hom., cov: 32)
• Consequence: BTBD10 NM_032320.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

BTBD10 (HGNC:21445): (BTB domain containing 10) Predicted to be involved in negative regulation of neuron death; positive regulation of phosphorylation; and type B pancreatic cell proliferation. Located in fibrillar center and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTBD10	NM_032320.7	c.101+7717G>T		intron_variant		ENST00000278174.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTBD10	ENST00000278174.10	c.101+7717G>T		intron_variant		1	NM_032320.7	P1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94428 AN: 151904 Hom.: 29975 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.629

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.622 AC: 94489 AN: 152022 Hom.: 29990 Cov.: 32 AF XY: 0.621 AC XY: 46119 AN XY: 74320

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.626

Alfa AF: 0.668 Hom.: 14797

Bravo AF: 0.604

Asia WGS AF: 0.515 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.7
Dann	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs730414; hg19: chr11-13458854;