10-76151274-A-T

Position:

• chr10-76151274-A-T

Variant summary

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

The NM_001305581.2(LRMDA):​c.516+92491A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,272 control chromosomes in the GnomAD database, including 64,892 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 0.92 (64892 hom., cov: 32)
• Consequence: LRMDA NM_001305581.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRMDA	NM_001305581.2	c.516+92491A>T		intron_variant		ENST00000611255.5
LRMDA	NM_032024.5	c.432+92491A>T		intron_variant
LRMDA	NR_131178.2	n.870+92491A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRMDA	ENST00000611255.5	c.516+92491A>T		intron_variant		5	NM_001305581.2	P1
LRMDA	ENST00000372499.5	c.432+92491A>T		intron_variant		1
LRMDA	ENST00000593699.5	n.870+92491A>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140348 AN: 152154 Hom.: 64829 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.917

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.923 AC: 140471 AN: 152272 Hom.: 64892 Cov.: 32 AF XY: 0.925 AC XY: 68858 AN XY: 74440

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.918

Alfa AF: 0.914 Hom.: 7978

Bravo AF: 0.926

Asia WGS AF: 0.985 AC: 3427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.30

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: rs10740455; hg19: chr10-77911032;