1-11068039-T-C

Variant names:

• chr1-11068039-T-C
• NM_001001998.3:c.2596A>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001001998.3(EXOSC10):​c.2596A>G​(p.Ser866Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: EXOSC10 NM_001001998.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.83

Genes affected

EXOSC10 (HGNC:9138): (exosome component 10) Enables 3'-5'-exoribonuclease activity. Involved in several processes, including RNA catabolic process; maturation of 5.8S rRNA; and negative regulation of telomere maintenance via telomerase. Located in cytosol; nuclear lumen; and transcriptionally active chromatin. Part of nuclear exosome (RNase complex). [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EXOSC10	NM_001001998.3	c.2596A>G	p.Ser866Gly	missense_variant	Exon 24 of 25	ENST00000376936.9	NP_001001998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EXOSC10	ENST00000376936.9	c.2596A>G	p.Ser866Gly	missense_variant	Exon 24 of 25	1	NM_001001998.3	ENSP00000366135.4
EXOSC10	ENST00000304457.11	c.2521A>G	p.Ser841Gly	missense_variant	Exon 23 of 24	1		ENSP00000307307.7
EXOSC10	ENST00000474216.5	n.1848A>G		non_coding_transcript_exon_variant	Exon 12 of 13	2
EXOSC10	ENST00000490565.1	n.326A>G		non_coding_transcript_exon_variant	Exon 2 of 3	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Nov 27, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2596A>G (p.S866G) alteration is located in exon 24 (coding exon 24) of the EXOSC10 gene. This alteration results from a A to G substitution at nucleotide position 2596, causing the serine (S) at amino acid position 866 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Uncertain	0.069	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.40	.;T
Eigen	Uncertain	0.52
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.85	T;D
M_CAP	Benign	0.025	D
MetaRNN	Uncertain	0.66	D;D
MetaSVM	Benign	-0.48	T
MutationAssessor	Uncertain	2.2	.;M
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-1.8	N;N
REVEL	Benign	0.15
Sift	Pathogenic	0.0	D;D
Sift4G	Benign	0.098	T;T
Polyphen		1.0	D;D
Vest4		0.70
MutPred		0.12		.;Loss of phosphorylation at S866 (P = 0.0346);
MVP		0.81
MPC		0.79
ClinPred		0.95	D
GERP RS		5.0
Varity_R		0.55
gMVP		0.31

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-11128096;