rs730414

Variant names:

• chr11-13437307-C-A
• rs730414
• NM_032320.7:c.101+7717G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BTBD10	NM_032320.7	c.101+7717G>T		intron_variant	Intron 2 of 8	ENST00000278174.10	NP_115696.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTBD10	ENST00000278174.10	c.101+7717G>T		intron_variant	Intron 2 of 8	1	NM_032320.7	ENSP00000278174.5

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

African (AFR) AF: 0.574 AC: 23815 AN: 41456

American (AMR) AF: 0.538 AC: 8213 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2516 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5166

South Asian (SAS) AF: 0.694 AC: 3343 AN: 4820

European-Finnish (FIN) AF: 0.658 AC: 6953 AN: 10572

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45914 AN: 67960

Other (OTH) AF: 0.626 AC: 1319 AN: 2108

Alfa AF: 0.667 Hom.: 16627

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs730414; hg19: chr11-13458854;