3-43476675-T-G

Position:

• chr3-43476675-T-G

Variant summary

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

The NM_018075.5(ANO10):​c.1798-43948A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,986 control chromosomes in the GnomAD database, including 20,641 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 0.49 (20641 hom., cov: 32)
• Consequence: ANO10 NM_018075.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

Genes affected

ANO10 (HGNC:25519): (anoctamin 10) The transmembrane protein encoded by this gene belongs to the anoctamin family of calcium-activated chloride channels, also known as the transmembrane 16 family. The encoded protein contains eight transmembrane domains with cytosolic N- and C-termini. Defects in this gene may cause autosomal recessive spinocerebellar ataxia-10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANO10	NM_018075.5	c.1798-43948A>C		intron_variant		ENST00000292246.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANO10	ENST00000292246.8	c.1798-43948A>C		intron_variant		1	NM_018075.5	P1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75025 AN: 151868 Hom.: 20633 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.494 AC: 75064 AN: 151986 Hom.: 20641 Cov.: 32 AF XY: 0.500 AC XY: 37173 AN XY: 74300

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.518

Alfa AF: 0.542 Hom.: 11103

Bravo AF: 0.480

Asia WGS AF: 0.714 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.82

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: rs1351631; hg19: chr3-43518167;