10-76036113-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001305581.2(LRMDA):c.237C>T(p.Thr79=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000806 in 1,613,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
LRMDA
NM_001305581.2 synonymous
NM_001305581.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.57
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 10-76036113-C-T is Benign according to our data. Variant chr10-76036113-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1978952.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRMDA | NM_001305581.2 | c.237C>T | p.Thr79= | synonymous_variant | 3/7 | ENST00000611255.5 | NP_001292510.1 | |
LRMDA | NM_032024.5 | c.153C>T | p.Thr51= | synonymous_variant | 2/6 | NP_114413.1 | ||
LRMDA | NR_131178.2 | n.591C>T | non_coding_transcript_exon_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRMDA | ENST00000611255.5 | c.237C>T | p.Thr79= | synonymous_variant | 3/7 | 5 | NM_001305581.2 | ENSP00000480240 | P1 | |
LRMDA | ENST00000372499.5 | c.153C>T | p.Thr51= | synonymous_variant | 2/6 | 1 | ENSP00000361577 | |||
LRMDA | ENST00000593699.5 | n.591C>T | non_coding_transcript_exon_variant | 4/8 | 1 | |||||
LRMDA | ENST00000593817.1 | n.198C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251174Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135750
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461690Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727158
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74300
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 09, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at