rs7174616

chr15-51725899-A-C

Variant summary

Our verdict is Benign. Variant got -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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LYSMD2	NM_153374.3	c.274-778T>G		intron_variant		ENST00000267838.7
LYSMD2	NM_001143917.2	c.1-778T>G		intron_variant
LYSMD2	NM_001363969.2	c.1-778T>G		intron_variant
LYSMD2	XM_047432340.1	c.43-778T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYSMD2	ENST00000267838.7	c.274-778T>G		intron_variant		1	NM_153374.3	P1
LYSMD2	ENST00000454181.6	c.1-778T>G		intron_variant		1
LYSMD2	ENST00000558126.1	c.83-908T>G		intron_variant		5
LYSMD2	ENST00000560491.2	c.1-778T>G		intron_variant		3

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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0326

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0529 Hom.: 347

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

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;