15-51725899-A-C

Variant names:

• chr15-51725899-A-C
• rs7174616
• NM_153374.3:c.274-778T>G

Variant summary

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

The NM_153374.3(LYSMD2):​c.274-778T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 152,204 control chromosomes in the GnomAD database, including 489 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 0.072 (489 hom., cov: 32)
• Consequence: LYSMD2 NM_153374.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LYSMD2	NM_153374.3	c.274-778T>G		intron_variant	Intron 1 of 2	ENST00000267838.7	NP_699205.1
LYSMD2	NM_001143917.2	c.1-778T>G		intron_variant	Intron 1 of 2		NP_001137389.1
LYSMD2	NM_001363969.2	c.1-778T>G		intron_variant	Intron 1 of 2		NP_001350898.1
LYSMD2	XM_047432340.1	c.43-778T>G		intron_variant	Intron 1 of 2		XP_047288296.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYSMD2	ENST00000267838.7	c.274-778T>G		intron_variant	Intron 1 of 2	1	NM_153374.3	ENSP00000267838.3
LYSMD2	ENST00000454181.6	c.1-778T>G		intron_variant	Intron 1 of 2	1		ENSP00000410424.2
LYSMD2	ENST00000560491.2	c.1-778T>G		intron_variant	Intron 1 of 2	3		ENSP00000453933.1
LYSMD2	ENST00000558126.1	c.83-908T>G		intron_variant	Intron 1 of 2	5		ENSP00000452715.1

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10917 AN: 152086 Hom.: 480 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0502

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0720 AC: 10959 AN: 152204 Hom.: 489 Cov.: 32 AF XY: 0.0699 AC XY: 5202 AN XY: 74424

African (AFR) AF: 0.122 AC: 5082 AN: 41504

American (AMR) AF: 0.0326 AC: 498 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00577 AC: 20 AN: 3466

East Asian (EAS) AF: 0.0943 AC: 489 AN: 5186

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4828

European-Finnish (FIN) AF: 0.0690 AC: 732 AN: 10606

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3887 AN: 68006

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0553 Hom.: 493

Bravo AF: 0.0721

Asia WGS AF: 0.0960 AC: 333 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.33
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs7174616; hg19: chr15-52018096;