dbSNP rs3731055: LSM3:c.21+58C>T (chr3-14178939-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_014463.3(LSM3):c.21+58C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0167 in 1,595,208 control chromosomes in the GnomAD database, including 1,596 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 209 hom., cov: 33)

Exomes 𝑓: 0.016 ( 1387 hom. )

Consequence

LSM3
NM_014463.3 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.03

Variant links:

Genes affected

LSM3 (HGNC:17874): (LSM3 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]

LSM3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 3-14178939-C-T is Benign according to our data. Variant chr3-14178939-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1167092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSM3	NM_014463.3 link	c.21+58C>T		intron_variant	Intron 1 of 3	ENST00000306024.4	NP_055278.1	P62310

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSM3	ENST00000306024.4 link	c.21+58C>T		intron_variant	Intron 1 of 3	1	NM_014463.3	ENSP00000302160.3		P62310

Frequencies

GnomAD3 genomes

AF:

0.0223

AC:

3393

AN:

152134

Hom.:

208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00589

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0918

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.0375

Gnomad FIN

AF:

0.00829

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00441

Gnomad OTH

AF:

0.0196

GnomAD4 exome

AF:

0.0161

AC:

23195

AN:

1442956

Hom.:

1387

AF XY:

0.0160

AC XY:

11471

AN XY:

718972

show subpopulations

Gnomad4 AFR exome

AF:

0.00450

Gnomad4 AMR exome

AF:

0.122

Gnomad4 ASJ exome

AF:

0.00392

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.0300

Gnomad4 FIN exome

AF:

0.0115

Gnomad4 NFE exome

AF:

0.00404

Gnomad4 OTH exome

AF:

0.0221

GnomAD4 genome

AF:

0.0224

AC:

3406

AN:

152252

Hom.:

209

Cov.:

AF XY:

0.0256

AC XY:

1907

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00602

Gnomad4 AMR

AF:

0.0918

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.217

Gnomad4 SAS

AF:

0.0375

Gnomad4 FIN

AF:

0.00829

Gnomad4 NFE

AF:

0.00443

Gnomad4 OTH

AF:

0.0208

Alfa

AF:

0.0207

Hom.:

Bravo

AF:

0.0294

Asia WGS

AF:

0.117

AC:

409

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jun 09, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 21822670) -

Oct 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.9

DANN

Benign

0.75

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over