rs201409815

Variant names:

• chr1-36393868-C-A
• rs201409815
• NM_032881.3:c.262G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-36393868-C-A
• chr1-36393868-C-G
• chr1-36393868-C-T

Variant summary

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

The NM_032881.3(LSM10):​c.262G>T​(p.Val88Leu) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V88M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LSM10 NM_032881.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 1 publications found

Genes affected

LSM10 (HGNC:17562): (LSM10, U7 small nuclear RNA associated) Enables U7 snRNA binding activity. Involved in positive regulation of G1/S transition of mitotic cell cycle. Located in Cajal body. Part of U7 snRNP. [provided by Alliance of Genome Resources, Apr 2022]

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=0.18279159).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032881.3. 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
	LSM10	NM_032881.3	MANE Select	c.262G>T	p.Val88Leu	missense	Exon 2 of 2	NP_116270.1	Q969L4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSM10	ENST00000315732.3	TSL:1 MANE Select	c.262G>T	p.Val88Leu	missense	Exon 2 of 2	ENSP00000319341.2	Q969L4
	LSM10	ENST00000861455.1		c.262G>T	p.Val88Leu	missense	Exon 3 of 3	ENSP00000531514.1
	LSM10	ENST00000861456.1		c.262G>T	p.Val88Leu	missense	Exon 2 of 2	ENSP00000531515.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Uncertain	0.030	T
BayesDel_noAF	Benign	-0.19
CADD	Benign	18
DANN	Uncertain	0.99
DEOGEN2	Benign	0.042	T
Eigen	Benign	-0.037
Eigen_PC	Benign	0.16
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	D
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.18	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Uncertain	2.0	M
PhyloP100		2.2
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-1.7	N
REVEL	Benign	0.17
Sift	Benign	0.19	T
Sift4G	Benign	0.26	T
Polyphen		0.12	B
Vest4		0.15
MutPred		0.47		Gain of solvent accessibility (P = 0.0156)
MVP		0.53
MPC		0.62
ClinPred		0.71	D
GERP RS		6.1
Varity_R		0.46
gMVP		0.68
Mutation Taster		=57/43	polymorphism

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

Other links and lift over

dbSNP: rs201409815; hg19: chr1-36859469;