rs3751972

Variant names:

• chr17-27879388-C-A
• rs3751972
• NM_001076680.3:c.*85G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 33 publications found

Genes affected

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

ENSG00000266202 (HGNC:):

ENSG00000266527 (HGNC:58314):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001076680.3. 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
	LYRM9	NM_001076680.3	MANE Select	c.*85G>T		3_prime_UTR	Exon 4 of 4	NP_001070148.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYRM9	ENST00000379102.8	TSL:2 MANE Select	c.*85G>T		3_prime_UTR	Exon 4 of 4	ENSP00000368396.3
	ENSG00000266202	ENST00000582441.1	TSL:4	c.219+886G>T		intron	N/A	ENSP00000462879.1
	ENSG00000266527	ENST00000581901.1	TSL:2	n.417C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121608 AN: 152142 Hom.: 49413 Cov.: 34

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.: 18 AF XY: 0.743 AC XY: 474409 AN XY: 638290

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

GnomAD4 genome AF: 0.800 AC: 121742 AN: 152260 Hom.: 49485 Cov.: 34 AF XY: 0.802 AC XY: 59700 AN XY: 74434

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.50
PhyloP100		-1.0
Mutation Taster		=100/0	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: rs3751972; hg19: chr17-26206414; COSMIC: COSV66959149; COSMIC: COSV66959149;