Genetic Variant NM_016200.5:c.*82G>A (chr7-118192084-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.952

Publications

15 publications found

Variant links:

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]

LSM8 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSM8	NM_016200.5 link	c.*82G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000249299.7	NP_057284.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
LSM8	ENST00000249299.7 link	c.*82G>A	3_prime_UTR_variant	Exon 4 of 4	1	NM_016200.5	ENSP00000249299.2
LSM8	ENST00000422760.1 link	c.*82G>A	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000403811.1
LSM8	ENST00000424702.1 link	c.*3675G>A	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000395263.1

Frequencies

GnomAD3 genomes

AF:

0.725

AC:

109999

AN:

151710

Hom.:

40162

Cov.:

show subpopulations

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.:

AF XY:

0.704

AC XY:

276739

AN XY:

393226

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

7594

15188

22782

30376

37970

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7848

15696

23544

31392

39240

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.725

AC:

110110

AN:

151828

Hom.:

40217

Cov.:

AF XY:

0.734

AC XY:

54446

AN XY:

74224

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1524

3049

4573

6098

7622

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

836

1672

2508

3344

4180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.1

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over