rs7823144

chr8-38170677-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014462.3(LSM1):c.116-760C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,026 control chromosomes in the GnomAD database, including 2,753 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2753 hom., cov: 32)
• Consequence: LSM1 NM_014462.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

LSM1 (HGNC:20472): (LSM1 homolog, mRNA degradation associated) This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Increased expression of this gene may play a role in cellular transformation and the progression of several malignancies including lung cancer, mesothelioma and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LSM1	NM_014462.3	c.116-760C>T		intron_variant		ENST00000311351.9
LSM1	NR_045492.2	n.288+1288C>T		intron_variant, non_coding_transcript_variant
LSM1	NR_045493.1	n.248-760C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSM1	ENST00000311351.9	c.116-760C>T		intron_variant		1	NM_014462.3	P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24775 AN: 151908 Hom.: 2741 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0400

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0811

Gnomad OTH AF: 0.123

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24830 AN: 152026 Hom.: 2753 Cov.: 32 AF XY: 0.168 AC XY: 12453 AN XY: 74318

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0400

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.0812

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0935 Hom.: 1171

Bravo AF: 0.165

Asia WGS AF: 0.224 AC: 781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	17
Dann	Benign	0.71

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

Other links and lift over

dbSNP: rs7823144; hg19: chr8-38028195;