rs3751972

Positions:

• chr17-27879388-C-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000266202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LYRM9	NM_001076680.3	c.*85G>T		3_prime_UTR_variant	4/4	ENST00000379102.8	NP_001070148.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LYRM9	ENST00000379102	c.*85G>T		3_prime_UTR_variant	4/4	2	NM_001076680.3	ENSP00000368396.3
ENSG00000266202	ENST00000582441.1	c.219+886G>T		intron_variant		4		ENSP00000462879.1

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

Gnomad4 AFR exome AF: 0.958

Gnomad4 AMR exome AF: 0.767

Gnomad4 ASJ exome AF: 0.743

Gnomad4 EAS exome AF: 0.577

Gnomad4 SAS exome AF: 0.803

Gnomad4 FIN exome AF: 0.788

Gnomad4 NFE exome AF: 0.735

Gnomad4 OTH exome AF: 0.737

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

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.772

Alfa AF: 0.749 Hom.: 39822

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
DANN	Benign	0.50

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: rs3751972; hg19: chr17-26206414; COSMIC: COSV66959149; COSMIC: COSV66959149;