rs971600555

Variant names:

• chr19-2324127-C-G
• NM_016199.3:c.167G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-2324127-C-G
• chr19-2324127-C-T

Variant summary

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

The NM_016199.3(LSM7):​c.167G>C​(p.Arg56Pro) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000707 in 1,413,918 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: LSM7 NM_016199.3 missense, splice_region
• Scores: Splicing: ADA: 0.6555
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.70

Genes affected

LSM7 (HGNC:20470): (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated) Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.[supplied by OMIM, Apr 2004]

ENSG00000273734 (HGNC:):

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
LSM7	NM_016199.3	c.167G>C	p.Arg56Pro	missense_variant, splice_region_variant	Exon 3 of 4	ENST00000252622.15	NP_057283.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSM7	ENST00000252622.15	c.167G>C	p.Arg56Pro	missense_variant, splice_region_variant	Exon 3 of 4	1	NM_016199.3	ENSP00000252622.8
ENSG00000273734	ENST00000621615.1	n.147-10475C>G		intron_variant	Intron 1 of 7	2		ENSP00000481965.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 7.07e-7 AC: 1 AN: 1413918 Hom.: 0 Cov.: 33 AF XY: 0.00000143 AC XY: 1 AN XY: 698980

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000125

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Benign	-0.090
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.64	D;T
Eigen	Benign	0.18
Eigen_PC	Uncertain	0.24
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.90	D;D
M_CAP	Benign	0.079	D
MetaRNN	Uncertain	0.60	D;D
MetaSVM	Benign	-0.88	T
MutationAssessor	Uncertain	2.6	M;.
PrimateAI	Pathogenic	0.80	T
PROVEAN	Pathogenic	-6.6	D;.
REVEL	Benign	0.14
Sift	Uncertain	0.026	D;.
Sift4G	Uncertain	0.046	D;D
Polyphen		0.35	B;.
Vest4		0.68
MutPred		0.47		Loss of stability (P = 0.0358);.;
MVP		0.69
MPC		1.5
ClinPred		0.99	D
GERP RS		5.0
Varity_R		0.86
gMVP		0.89

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.66
dbscSNV1_RF	Benign	0.59
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: chr19-2324126;