7-118192084-G-A

Variant names:

• chr7-118192084-G-A
• rs1061731
• NM_016200.5:c.*82G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 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.*82G>A		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.*82G>A		3_prime_UTR	Exon 4 of 4	ENSP00000249299.2
	LSM8	ENST00000422760.1	TSL:1	c.*82G>A		3_prime_UTR	Exon 3 of 3	ENSP00000403811.1
	LSM8	ENST00000424702.1	TSL:1	c.*3675G>A		3_prime_UTR	Exon 3 of 3	ENSP00000395263.1

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

African (AFR) AF: 0.772 AC: 13517 AN: 17518

American (AMR) AF: 0.776 AC: 16822 AN: 21688

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 11270 AN: 17602

East Asian (EAS) AF: 0.806 AC: 24919 AN: 30898

South Asian (SAS) AF: 0.834 AC: 36897 AN: 44254

European-Finnish (FIN) AF: 0.792 AC: 34715 AN: 43834

Middle Eastern (MID) AF: 0.735 AC: 2956 AN: 4022

European-Non Finnish (NFE) AF: 0.673 AC: 372535 AN: 553790

Other (OTH) AF: 0.702 AC: 24888 AN: 35450

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

African (AFR) AF: 0.769 AC: 31816 AN: 41378

American (AMR) AF: 0.743 AC: 11338 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3466

East Asian (EAS) AF: 0.778 AC: 4019 AN: 5164

South Asian (SAS) AF: 0.847 AC: 4079 AN: 4818

European-Finnish (FIN) AF: 0.802 AC: 8466 AN: 10550

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45920 AN: 67886

Other (OTH) AF: 0.698 AC: 1476 AN: 2114

Alfa AF: 0.686 Hom.: 35888

Bravo AF: 0.719

Asia WGS AF: 0.813 AC: 2821 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.28
PhyloP100		0.95
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1061731; hg19: chr7-117832138;