Variant 5-10249898-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000509915.1(ENSG00000248968):n.671A>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 0.0131 in 818,222 control chromosomes in the GnomAD database, including 168 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 29 hom., cov: 0)

Exomes 𝑓: 0.012 ( 139 hom. )

Consequence

ENST00000509915.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.677

Variant links:

Genes affected

(HGNC:):

links:

ATPSCKMT (HGNC:27029): (ATP synthase c subunit lysine N-methyltransferase) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation; positive regulation of sensory perception of pain; and regulation of proton transport. Located in mitochondrial crista. [provided by Alliance of Genome Resources, Apr 2022]

ATPSCKMT links:

CCT5 (HGNC:1618): (chaperonin containing TCP1 subunit 5) The protein encoded by this gene is a molecular chaperone that is a member of the chaperonin containing TCP1 complex (CCT), also known as the TCP1 ring complex (TRiC). This complex consists of two identical stacked rings, each containing eight different proteins. Unfolded polypeptides enter the central cavity of the complex and are folded in an ATP-dependent manner. The complex folds various proteins, including actin and tubulin. Mutations in this gene cause hereditary sensory and autonomic neuropathy with spastic paraplegia (HSNSP). Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 5 and 13. [provided by RefSeq, Apr 2015]

CCT5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 5-10249898-A-T is Benign according to our data. Variant chr5-10249898-A-T is described in ClinVar as [Benign]. Clinvar id is 1272001.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATPSCKMT	NM_199133.4 linkuse as main transcript			upstream_gene_variant		ENST00000511437.6	NP_954584.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000509915.1 linkuse as main transcript	n.671A>T		non_coding_transcript_exon_variant	2/2	3
ATPSCKMT	ENST00000511437.6 linkuse as main transcript			upstream_gene_variant		1	NM_199133.4	ENSP00000422338	P1	Q6P4H8-1

Frequencies

GnomAD3 genomes

AF:

0.0679

AC:

1481

AN:

21820

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0668

Gnomad ASJ

AF:

0.0423

Gnomad EAS

AF:

0.0517

Gnomad SAS

AF:

0.0640

Gnomad FIN

AF:

0.0145

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0450

Gnomad OTH

AF:

0.0876

GnomAD3 exomes

AF:

0.157

AC:

2627

AN:

16728

Hom.:

AF XY:

0.160

AC XY:

1403

AN XY:

8794

show subpopulations

Gnomad AFR exome

AF:

0.323

Gnomad AMR exome

AF:

0.0832

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.144

Gnomad SAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.0544

Gnomad NFE exome

AF:

0.211

Gnomad OTH exome

AF:

0.153

GnomAD4 exome

AF:

0.0116

AC:

9234

AN:

796404

Hom.:

139

Cov.:

AF XY:

0.0121

AC XY:

4690

AN XY:

387296

show subpopulations

Gnomad4 AFR exome

AF:

0.0614

Gnomad4 AMR exome

AF:

0.0288

Gnomad4 ASJ exome

AF:

0.0176

Gnomad4 EAS exome

AF:

0.0108

Gnomad4 SAS exome

AF:

0.0176

Gnomad4 FIN exome

AF:

0.0316

Gnomad4 NFE exome

AF:

0.00965

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0679

AC:

1482

AN:

21818

Hom.:

Cov.:

AF XY:

0.0638

AC XY:

687

AN XY:

10774

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.0666

Gnomad4 ASJ

AF:

0.0423

Gnomad4 EAS

AF:

0.0526

Gnomad4 SAS

AF:

0.0630

Gnomad4 FIN

AF:

0.0145

Gnomad4 NFE

AF:

0.0450

Gnomad4 OTH

AF:

0.0882

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.74

DANN

Benign

0.44

Splicing

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