NM_001363580.1:c.116G>C

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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. 8/12 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

Genes affected

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

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C10orf95	NM_001363580.1	c.116G>C	p.Ser39Thr	missense_variant	Exon 2 of 2	ENST00000625129.1	NP_001350509.1
C10orf95-AS1	NR_038937.1	n.381-421C>G		intron_variant	Intron 2 of 4
C10orf95-AS1	NR_038938.1	n.350+648C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C10orf95	ENST00000625129.1	c.116G>C	p.Ser39Thr	missense_variant	Exon 2 of 2	1	NM_001363580.1	ENSP00000489684.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
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
GERP RS		0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
gMVP		0.029

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2281878; hg19: chr10-104210735;