15-51737469-A-G

Variant names:

• chr15-51737469-A-G
• NM_153374.3:c.154T>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_153374.3(LYSMD2):​c.154T>C​(p.Tyr52His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LYSMD2 NM_153374.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.62
• Publications: 0 publications found

Genes affected

LYSMD2 (HGNC:28571): (LysM domain containing 2)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153374.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYSMD2	NM_153374.3	MANE Select	c.154T>C	p.Tyr52His	missense	Exon 1 of 3	NP_699205.1	Q8IV50-1
	LYSMD2	NM_001143917.2		c.1-12348T>C		intron	N/A	NP_001137389.1	Q8IV50-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYSMD2	ENST00000267838.7	TSL:1 MANE Select	c.154T>C	p.Tyr52His	missense	Exon 1 of 3	ENSP00000267838.3	Q8IV50-1
	LYSMD2	ENST00000454181.6	TSL:1	c.1-12348T>C		intron	N/A	ENSP00000410424.2	Q8IV50-2
	LYSMD2	ENST00000875743.1		c.154T>C	p.Tyr52His	missense	Exon 1 of 3	ENSP00000545802.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1271144 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 625398

African (AFR) AF: 0.00 AC: 0 AN: 25436

American (AMR) AF: 0.00 AC: 0 AN: 20774

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21142

East Asian (EAS) AF: 0.00 AC: 0 AN: 26954

South Asian (SAS) AF: 0.00 AC: 0 AN: 66772

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31410

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3698

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1022980

Other (OTH) AF: 0.00 AC: 0 AN: 51978

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Benign	0.0024	T
BayesDel_noAF	Benign	-0.23
CADD	Pathogenic	30
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.47	T
Eigen	Uncertain	0.34
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Uncertain	0.88	D
M_CAP	Pathogenic	0.57	D
MetaRNN	Uncertain	0.48	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.2	M
PhyloP100		7.6
PrimateAI	Pathogenic	0.97	D
PROVEAN	Uncertain	-3.6	D
REVEL	Uncertain	0.30
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.47
MutPred		0.35		Loss of sheet (P = 0.0126)
MVP		0.36
MPC		0.65
ClinPred		0.99	D
GERP RS		4.0
PromoterAI		-0.030	Neutral
Varity_R		0.66
gMVP		0.59

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

hg19: chr15-52029666;