rs11001720

chr10-76289603-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.517-34798C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,934 control chromosomes in the GnomAD database, including 24,449 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 0.55 (24449 hom., cov: 31)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRMDA	NM_001305581.2	c.517-34798C>T		intron_variant		ENST00000611255.5
LOC124902462	XR_007062203.1	n.441G>A		non_coding_transcript_exon_variant	3/3
LRMDA	NM_032024.5	c.433-34798C>T		intron_variant
LRMDA	NR_131178.2	n.871-34798C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRMDA	ENST00000611255.5	c.517-34798C>T		intron_variant		5	NM_001305581.2	P1
LRMDA	ENST00000372499.5	c.433-34798C>T		intron_variant		1
LRMDA	ENST00000593699.5	n.871-34798C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84051 AN: 151818 Hom.: 24404 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.554 AC: 84150 AN: 151934 Hom.: 24449 Cov.: 31 AF XY: 0.553 AC XY: 41042 AN XY: 74236

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.555

Alfa AF: 0.514 Hom.: 3514

Bravo AF: 0.568

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.57
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: rs11001720; hg19: chr10-78049361;