rs11001716

chr10-76275034-G-Achr10-76275034-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001305581.2(LRMDA):c.517-49367G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,970 control chromosomes in the GnomAD database, including 18,931 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 0.50 (18931 hom., cov: 32)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

Genes affected

LRMDA (HGNC:23405): (leucine rich melanocyte differentiation associated) This gene encodes a leucine-rich repeat protein. The encoded protein is thought to play a role in melanocyte differentiation. Mutations in this gene have been associated with autosomal recessive oculocutaneous albinism 7 (OCA7). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRMDA	NM_001305581.2	c.517-49367G>A		intron_variant		ENST00000611255.5
LRMDA	NM_032024.5	c.433-49367G>A		intron_variant
LRMDA	NR_131178.2	n.871-49367G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRMDA	ENST00000611255.5	c.517-49367G>A		intron_variant		5	NM_001305581.2	P1
LRMDA	ENST00000372499.5	c.433-49367G>A		intron_variant		1
LRMDA	ENST00000593699.5	n.871-49367G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75290 AN: 151852 Hom.: 18907 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.496 AC: 75344 AN: 151970 Hom.: 18931 Cov.: 32 AF XY: 0.496 AC XY: 36878 AN XY: 74294

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.506

Alfa AF: 0.377 Hom.: 1794

Bravo AF: 0.502

Asia WGS AF: 0.588 AC: 2044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.4
Dann	Benign	0.17

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: rs11001716; hg19: chr10-78034792;