10-76356341-G-T

Position:

• chr10-76356341-G-T

Variant summary

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

The NM_001305581.2(LRMDA):​c.601+31856G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,020 control chromosomes in the GnomAD database, including 9,575 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 0.30 (9575 hom., cov: 32)
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRMDA	NM_001305581.2	c.601+31856G>T		intron_variant		ENST00000611255.5	NP_001292510.1
LRMDA	NM_032024.5	c.517+31856G>T		intron_variant			NP_114413.1
LRMDA	NR_131178.2	n.955+31856G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRMDA	ENST00000611255.5	c.601+31856G>T		intron_variant		5	NM_001305581.2	ENSP00000480240	P1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45541 AN: 151902 Hom.: 9551 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.300 AC: 45612 AN: 152020 Hom.: 9575 Cov.: 32 AF XY: 0.303 AC XY: 22475 AN XY: 74288

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.278

Alfa AF: 0.168 Hom.: 3414

Bravo AF: 0.305

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.78

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: rs9299535; hg19: chr10-78116099;