10-76202596-T-C

Position:

• chr10-76202596-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001305581.2(LRMDA):​c.517-121805T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,834 control chromosomes in the GnomAD database, including 9,347 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 0.31 (9347 hom., cov: 32)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRMDA	NM_001305581.2	c.517-121805T>C		intron_variant		ENST00000611255.5	NP_001292510.1
LRMDA	NM_032024.5	c.433-121805T>C		intron_variant			NP_114413.1
LRMDA	NR_131178.2	n.871-121805T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRMDA	ENST00000611255.5	c.517-121805T>C		intron_variant		5	NM_001305581.2	ENSP00000480240	P1
LRMDA	ENST00000372499.5	c.433-121805T>C		intron_variant		1		ENSP00000361577
LRMDA	ENST00000593699.5	n.871-121805T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47549 AN: 151716 Hom.: 9311 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.314 AC: 47657 AN: 151834 Hom.: 9347 Cov.: 32 AF XY: 0.318 AC XY: 23584 AN XY: 74200

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.312

Alfa AF: 0.241 Hom.: 2189

Bravo AF: 0.332

Asia WGS AF: 0.476 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	18
DANN	Benign	0.75

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: rs11001685; hg19: chr10-77962354;