rs10500780

Positions:

• chr11-13401400-C-A
• chr11-13401400-C-T

Variant summary

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

The NM_032320.7(BTBD10):​c.1117+1768G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,006 control chromosomes in the GnomAD database, including 1,546 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 0.13 (1546 hom., cov: 31)
• Consequence: BTBD10 NM_032320.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTBD10	NM_032320.7	c.1117+1768G>T		intron_variant		ENST00000278174.10	NP_115696.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTBD10	ENST00000278174.10	c.1117+1768G>T		intron_variant		1	NM_032320.7	ENSP00000278174	P1
BTBD10	ENST00000528120.5	c.973+1768G>T		intron_variant		2		ENSP00000435257
BTBD10	ENST00000530907.5	c.1141+1768G>T		intron_variant		2		ENSP00000431186
BTBD10	ENST00000527102.6	c.*419+1768G>T		intron_variant, NMD_transcript_variant		2		ENSP00000435303

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19316 AN: 151890 Hom.: 1544 Cov.: 31

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.127 AC: 19323 AN: 152006 Hom.: 1546 Cov.: 31 AF XY: 0.132 AC XY: 9807 AN XY: 74260

Gnomad4 AFR AF: 0.0437

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.148

Alfa AF: 0.120 Hom.: 406

Bravo AF: 0.115

Asia WGS AF: 0.213 AC: 737 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.63

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: rs10500780; hg19: chr11-13422947;