7-118198109-G-T

Variant names:

• chr7-118198109-G-T
• rs12537795
• NM_016200.5:c.*6107G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016200.5(LSM8):​c.*6107G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,958 control chromosomes in the GnomAD database, including 36,987 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 0.70 (36987 hom., cov: 31)
• Consequence: LSM8 NM_016200.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 4 publications found

Genes affected

LSM8 (HGNC:20471): (LSM8 homolog, U6 small nuclear RNA associated) This gene encodes a member of the like-Sm family of proteins. The encoded protein consists of a closed barrel shape, made up of five anti-parallel beta strands and an alpha helix. This protein partners with six paralogs to form a heteroheptameric ring which transiently binds U6 small nuclear RNAs and is involved in the general maturation of RNA in the nucleus. [provided by RefSeq, Jan 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016200.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSM8	NM_016200.5	MANE Select	c.*6107G>T		3_prime_UTR	Exon 4 of 4	NP_057284.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LSM8	ENST00000249299.7	TSL:1 MANE Select	c.*6107G>T		3_prime_UTR	Exon 4 of 4	ENSP00000249299.2

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105635 AN: 151840 Hom.: 36934 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.696 AC: 105743 AN: 151958 Hom.: 36987 Cov.: 31 AF XY: 0.704 AC XY: 52255 AN XY: 74266

African (AFR) AF: 0.713 AC: 29551 AN: 41450

American (AMR) AF: 0.697 AC: 10623 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2125 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3614 AN: 5162

South Asian (SAS) AF: 0.816 AC: 3929 AN: 4816

European-Finnish (FIN) AF: 0.792 AC: 8377 AN: 10574

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45318 AN: 67928

Other (OTH) AF: 0.670 AC: 1412 AN: 2108

Alfa AF: 0.678 Hom.: 9596

Bravo AF: 0.684

Asia WGS AF: 0.760 AC: 2632 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.59
PhyloP100		-0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12537795; hg19: chr7-117838163;