rs1061731

Positions:

• chr7-118192084-G-A
• chr7-118192084-G-C
• chr7-118192084-G-T

Variant summary

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

The NM_016200.5(LSM8):​c.*82G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 920,884 control chromosomes in the GnomAD database, including 230,130 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 0.73 (40217 hom., cov: 30)
  • Exomes 𝑓: 0.70 (189913 hom.)
• Consequence: LSM8 NM_016200.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.952

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LSM8	NM_016200.5	c.*82G>A		3_prime_UTR_variant	4/4	ENST00000249299.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LSM8	ENST00000249299.7	c.*82G>A		3_prime_UTR_variant	4/4	1	NM_016200.5	P1
LSM8	ENST00000422760.1	c.*82G>A		3_prime_UTR_variant	3/3	1
LSM8	ENST00000424702.1	c.*3675G>A		3_prime_UTR_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 109999 AN: 151710 Hom.: 40162 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.697

GnomAD4 exome AF: 0.700 AC: 538519 AN: 769056 Hom.: 189913 Cov.: 10 AF XY: 0.704 AC XY: 276739 AN XY: 393226

Gnomad4 AFR exome AF: 0.772

Gnomad4 AMR exome AF: 0.776

Gnomad4 ASJ exome AF: 0.640

Gnomad4 EAS exome AF: 0.806

Gnomad4 SAS exome AF: 0.834

Gnomad4 FIN exome AF: 0.792

Gnomad4 NFE exome AF: 0.673

Gnomad4 OTH exome AF: 0.702

GnomAD4 genome AF: 0.725 AC: 110110 AN: 151828 Hom.: 40217 Cov.: 30 AF XY: 0.734 AC XY: 54446 AN XY: 74224

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.698

Alfa AF: 0.685 Hom.: 29512

Bravo AF: 0.719

Asia WGS AF: 0.813 AC: 2821 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.28
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0

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: rs1061731; hg19: chr7-117832138;