rs10085904

Positions:

• chr7-118194920-A-C
• chr7-118194920-A-G
• chr7-118194920-A-T

Variant summary

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

The ENST00000249299.7(LSM8):​c.*2918A>C 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 151,968 control chromosomes in the GnomAD database, including 36,968 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 (36968 hom., cov: 31)
• Consequence: LSM8 ENST00000249299.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LSM8	NM_016200.5	c.*2918A>C		3_prime_UTR_variant	4/4	ENST00000249299.7	NP_057284.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LSM8	ENST00000249299.7	c.*2918A>C		3_prime_UTR_variant	4/4	1	NM_016200.5	ENSP00000249299	P1

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105602 AN: 151850 Hom.: 36915 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.814

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: 105710 AN: 151968 Hom.: 36968 Cov.: 31 AF XY: 0.703 AC XY: 52231 AN XY: 74268

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.669

Alfa AF: 0.682 Hom.: 8826

Bravo AF: 0.684

Asia WGS AF: 0.760 AC: 2639 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	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10085904; hg19: chr7-117834974;