10-102450978-C-G

Variant names:

• chr10-102450978-C-G
• rs2281878
• NM_001363580.1:c.116G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001363580.1(C10orf95):​c.116G>C​(p.Ser39Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C10orf95 NM_001363580.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 13 publications found

Genes affected

C10orf95 (HGNC:25880): (chromosome 10 open reading frame 95)

C10orf95-AS1 (HGNC:45238): (C10orf95 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19664422).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363580.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf95	NM_001363580.1	MANE Select	c.116G>C	p.Ser39Thr	missense	Exon 2 of 2	NP_001350509.1
	C10orf95-AS1	NR_038937.1		n.381-421C>G		intron	N/A
	C10orf95-AS1	NR_038938.1		n.350+648C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C10orf95	ENST00000625129.1	TSL:1 MANE Select	c.116G>C	p.Ser39Thr	missense	Exon 2 of 2	ENSP00000489684.1
	C10orf95-AS1	ENST00000473970.4	TSL:1	n.351+648C>G		intron	N/A
	C10orf95-AS1	ENST00000492465.2	TSL:1	n.345-421C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.96
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.40
FATHMM_MKL	Benign	0.47	N
LIST_S2	Benign	0.23	T
M_CAP	Benign	0.033	D
MetaRNN	Benign	0.20	T
PhyloP100		-0.20
GERP RS		0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
gMVP		0.029
Mutation Taster		=98/2	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2281878; hg19: chr10-104210735;