chr8-38173827-A-G

Position:

• chr8-38173827-A-G

Variant summary

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

The NM_014462.3(LSM1):​c.47-1794T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,190 control chromosomes in the GnomAD database, including 3,508 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 0.20 (3508 hom., cov: 32)
• Consequence: LSM1 NM_014462.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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]

LSM1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LSM1	NM_014462.3	c.47-1794T>C		intron_variant		ENST00000311351.9	NP_055277.1
LSM1	NR_045492.2	n.220-1794T>C		intron_variant
LSM1	NR_045493.1	n.179-1794T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSM1	ENST00000311351.9	c.47-1794T>C		intron_variant		1	NM_014462.3	ENSP00000310596.4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31160 AN: 152072 Hom.: 3505 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.205 AC: 31173 AN: 152190 Hom.: 3508 Cov.: 32 AF XY: 0.201 AC XY: 14932 AN XY: 74412

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.205

Alfa AF: 0.234 Hom.: 9327

Bravo AF: 0.208

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.64
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs16887244; hg19: chr8-38031345;