rs7080160

Positions:

• chr10-75779415-T-G

Variant summary

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

The NM_001305581.2(LRMDA):​c.132-256593T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,998 control chromosomes in the GnomAD database, including 12,861 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 0.38 (12861 hom., cov: 32)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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]

LRMDA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRMDA	NM_001305581.2	c.132-256593T>G		intron_variant		ENST00000611255.5	NP_001292510.1
LRMDA	NR_131178.2	n.86-103241T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRMDA	ENST00000611255.5	c.132-256593T>G		intron_variant		5	NM_001305581.2	ENSP00000480240.1
LRMDA	ENST00000593699.5	n.86-103241T>G		intron_variant		1
LRMDA	ENST00000593817.1	n.92+178084T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57545 AN: 151880 Hom.: 12851 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.379 AC: 57570 AN: 151998 Hom.: 12861 Cov.: 32 AF XY: 0.384 AC XY: 28525 AN XY: 74296

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.369

Alfa AF: 0.436 Hom.: 1970

Bravo AF: 0.356

Asia WGS AF: 0.414 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	10
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7080160; hg19: chr10-77539173;