Variant chr22-45671813-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2

The ENST00000623075.1(ENSG00000280383):n.14795C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0372 in 332,136 control chromosomes in the GnomAD database, including 293 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.037 ( 122 hom., cov: 31)

Exomes 𝑓: 0.037 ( 171 hom. )

Consequence

ENST00000623075.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.29

Variant links:

Genes affected

(HGNC:):

links:

ATXN10 (HGNC:10549): (ataxin 10) This gene encodes a protein that may function in neuron survival, neuron differentiation, and neuritogenesis. These roles may be carried out via activation of the mitogen-activated protein kinase cascade. Expansion of an ATTCT repeat from 9-32 copies to 800-4500 copies in an intronic region of this locus has been associated with spinocerebellar ataxia, type 10. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jul 2016]

ATXN10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant 22-45671813-C-T is Benign according to our data. Variant chr22-45671813-C-T is described in ClinVar as [Benign]. Clinvar id is 1228260.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0371 (5633/151944) while in subpopulation NFE AF= 0.0396 (2690/67890). AF 95% confidence interval is 0.0384. There are 122 homozygotes in gnomad4. There are 2865 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 122 gene

Transcripts

RefSeq

Gene	Transcript	Effect	MANE
ATXN10	NM_013236.4 linkuse as main transcript	upstream_gene_variant	ENST00000252934.10
ATXN10	NM_001167621.2 linkuse as main transcript	upstream_gene_variant
ATXN10	XM_047441314.1 linkuse as main transcript	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623075.1 linkuse as main transcript	n.14795C>T	non_coding_transcript_exon_variant	1/1
ATXN10	ENST00000381061.8 linkuse as main transcript	c.-251C>T	5_prime_UTR_variant	1/11	2			Q9UBB4-2
ATXN10	ENST00000252934.10 linkuse as main transcript		upstream_gene_variant		1	NM_013236.4	P1	Q9UBB4-1

Frequencies

GnomAD3 genomes

AF:

0.0370

AC:

5624

AN:

151828

Hom.:

122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0308

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0384

Gnomad ASJ

AF:

0.0602

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.0187

Gnomad FIN

AF:

0.0652

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0396

Gnomad OTH

AF:

0.0358

GnomAD4 exome

AF:

0.0374

AC:

6735

AN:

180192

Hom.:

171

Cov.:

AF XY:

0.0371

AC XY:

3504

AN XY:

94472

show subpopulations

Gnomad4 AFR exome

AF:

0.0330

Gnomad4 AMR exome

AF:

0.0311

Gnomad4 ASJ exome

AF:

0.0642

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0255

Gnomad4 FIN exome

AF:

0.0585

Gnomad4 NFE exome

AF:

0.0397

Gnomad4 OTH exome

AF:

0.0376

GnomAD4 genome

AF:

0.0371

AC:

5633

AN:

151944

Hom.:

122

Cov.:

AF XY:

0.0386

AC XY:

2865

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.0309

Gnomad4 AMR

AF:

0.0384

Gnomad4 ASJ

AF:

0.0602

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.0192

Gnomad4 FIN

AF:

0.0652

Gnomad4 NFE

AF:

0.0396

Gnomad4 OTH

AF:

0.0359

Alfa

AF:

0.0352

Hom.:

Bravo

AF:

0.0351

Asia WGS

AF:

0.00779

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.95

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over