Genetic Variant NM_001076680.3:c.*85G>T (chr17-27879388-C-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_001076680.3(LYRM9):c.*85G>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 0.749 in 1,443,304 control chromosomes in the GnomAD database, including 407,561 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 0.80 ( 49485 hom., cov: 34)

Exomes 𝑓: 0.74 ( 358076 hom. )

Consequence

LYRM9
NM_001076680.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

33 publications found

Variant links:

Genes affected

LYRM9 (HGNC:27314): (LYR motif containing 9)

LYRM9 links:

ENSG00000266202 (HGNC:):

ENSG00000266202 links:

ENSG00000266527 (HGNC:58314):

ENSG00000266527 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYRM9	NM_001076680.3 link	c.*85G>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000379102.8	NP_001070148.1	A8MSI8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYRM9	ENST00000379102.8 link	c.*85G>T		3_prime_UTR_variant	Exon 4 of 4	2	NM_001076680.3	ENSP00000368396.3		A8MSI8
ENSG00000266202	ENST00000582441.1 link	c.219+886G>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1		J3KTA2

Frequencies

GnomAD3 genomes

AF:

0.799

AC:

121608

AN:

152142

Hom.:

49413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.946

Gnomad AMI

AF:

0.754

Gnomad AMR

AF:

0.787

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.543

Gnomad SAS

AF:

0.809

Gnomad FIN

AF:

0.794

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.736

Gnomad OTH

AF:

0.772

GnomAD4 exome

AF:

0.743

AC:

958725

AN:

1291044

Hom.:

358076

Cov.:

AF XY:

0.743

AC XY:

474409

AN XY:

638290

show subpopulations

African (AFR)

AF:

0.958

AC:

26557

AN:

27716

American (AMR)

AF:

0.767

AC:

20755

AN:

27058

Ashkenazi Jewish (ASJ)

AF:

0.743

AC:

16728

AN:

22528

East Asian (EAS)

AF:

0.577

AC:

19496

AN:

33790

South Asian (SAS)

AF:

0.803

AC:

56687

AN:

70602

European-Finnish (FIN)

AF:

0.788

AC:

36868

AN:

46788

Middle Eastern (MID)

AF:

0.782

AC:

3056

AN:

3906

European-Non Finnish (NFE)

AF:

0.735

AC:

738894

AN:

1004808

Other (OTH)

AF:

0.737

AC:

39684

AN:

53848

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

11222

22445

33667

44890

56112

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.800

AC:

121742

AN:

152260

Hom.:

49485

Cov.:

AF XY:

0.802

AC XY:

59700

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.946

AC:

39341

AN:

41580

American (AMR)

AF:

0.787

AC:

12045

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.749

AC:

2601

AN:

3472

East Asian (EAS)

AF:

0.543

AC:

2799

AN:

5154

South Asian (SAS)

AF:

0.810

AC:

3909

AN:

4824

European-Finnish (FIN)

AF:

0.794

AC:

8417

AN:

10598

Middle Eastern (MID)

AF:

0.810

AC:

238

AN:

294

European-Non Finnish (NFE)

AF:

0.736

AC:

50071

AN:

68012

Other (OTH)

AF:

0.772

AC:

1633

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1208

2415

3623

4830

6038

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.761

Hom.:

114365

Bravo

AF:

0.801

Asia WGS

AF:

0.721

AC:

2506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.22

(source)

DANN

Benign

0.50

PhyloP100

-1.0

Mutation Taster

=100/0

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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NM_001076680.3:c.*85G>T

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