chr17-64860117-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_199340.5(LRRC37A3):c.4029G>A(p.Pro1343=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000433 in 1,613,936 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00045 ( 5 hom. )
Consequence
LRRC37A3
NM_199340.5 synonymous
NM_199340.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.08
Genes affected
LRRC37A3 (HGNC:32427): (leucine rich repeat containing 37 member A3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 17-64860117-C-T is Benign according to our data. Variant chr17-64860117-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648102.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.09 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4029G>A | p.Pro1343= | synonymous_variant | 12/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+10130C>T | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.1383G>A | p.Pro461= | synonymous_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4029G>A | p.Pro1343= | synonymous_variant | 12/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152148Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000783 AC: 196AN: 250350Hom.: 1 AF XY: 0.00111 AC XY: 151AN XY: 135604
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GnomAD4 exome AF: 0.000455 AC: 665AN: 1461670Hom.: 5 Cov.: 33 AF XY: 0.000637 AC XY: 463AN XY: 727146
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GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152266Hom.: 0 Cov.: 31 AF XY: 0.000336 AC XY: 25AN XY: 74454
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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 | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | LRRC37A3: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at