rs2579790

Positions:

• chr10-76295966-C-A
• chr10-76295966-C-T

Variant summary

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

The NM_001305581.2(LRMDA):​c.517-28435C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,964 control chromosomes in the GnomAD database, including 21,102 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 0.51 (21102 hom., cov: 32)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

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]

LOC124902462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRMDA	NM_001305581.2	c.517-28435C>A		intron_variant		ENST00000611255.5	NP_001292510.1
LOC124902462	XR_007062203.1	n.151-6073G>T		intron_variant, non_coding_transcript_variant
LRMDA	NM_032024.5	c.433-28435C>A		intron_variant			NP_114413.1
LRMDA	NR_131178.2	n.871-28435C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRMDA	ENST00000611255.5	c.517-28435C>A		intron_variant		5	NM_001305581.2	ENSP00000480240	P1
LRMDA	ENST00000372499.5	c.433-28435C>A		intron_variant		1		ENSP00000361577
LRMDA	ENST00000593699.5	n.871-28435C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77323 AN: 151846 Hom.: 21094 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.0978

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.509 AC: 77370 AN: 151964 Hom.: 21102 Cov.: 32 AF XY: 0.499 AC XY: 37043 AN XY: 74300

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.0974

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.510

Alfa AF: 0.578 Hom.: 33295

Bravo AF: 0.501

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.64

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: rs2579790; hg19: chr10-78055724;