rs10509373

Positions:

• chr10-76397814-T-C

Variant summary

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

The NM_001305581.2(LRMDA):​c.601+73329T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,904 control chromosomes in the GnomAD database, including 9,767 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 0.32 (9767 hom., cov: 33)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

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=-0.6).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRMDA	NM_001305581.2	c.601+73329T>C		intron_variant		ENST00000611255.5
LRMDA	NM_032024.5	c.517+73329T>C		intron_variant
LRMDA	NR_131178.2	n.955+73329T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRMDA	ENST00000611255.5	c.601+73329T>C		intron_variant		5	NM_001305581.2	P1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48113 AN: 151786 Hom.: 9769 Cov.: 33

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.0406

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.317 AC: 48105 AN: 151904 Hom.: 9767 Cov.: 33 AF XY: 0.312 AC XY: 23145 AN XY: 74268

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.331

Alfa AF: 0.426 Hom.: 13220

Bravo AF: 0.310

Asia WGS AF: 0.119 AC: 415 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	12
DANN	Benign	0.72

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: rs10509373; hg19: chr10-78157572;