chr17-64859799-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_199340.5(LRRC37A3):c.4347C>T(p.Asn1449=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0025 in 1,612,180 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 42 hom., cov: 31)
Exomes 𝑓: 0.0014 ( 43 hom. )
Consequence
LRRC37A3
NM_199340.5 synonymous
NM_199340.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.417
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 17-64859799-G-A is Benign according to our data. Variant chr17-64859799-G-A is described in ClinVar as [Benign]. Clinvar id is 730719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.417 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0127 (1933/152016) while in subpopulation AFR AF= 0.0445 (1845/41422). AF 95% confidence interval is 0.0428. There are 42 homozygotes in gnomad4. There are 932 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 40 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4347C>T | p.Asn1449= | synonymous_variant | 12/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+9812G>A | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.1701C>T | p.Asn567= | synonymous_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4347C>T | p.Asn1449= | synonymous_variant | 12/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0127 AC: 1922AN: 151900Hom.: 40 Cov.: 31
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GnomAD3 exomes AF: 0.00334 AC: 836AN: 250030Hom.: 17 AF XY: 0.00249 AC XY: 338AN XY: 135528
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GnomAD4 exome AF: 0.00144 AC: 2097AN: 1460164Hom.: 43 Cov.: 33 AF XY: 0.00127 AC XY: 925AN XY: 726388
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GnomAD4 genome ? AF: 0.0127 AC: 1933AN: 152016Hom.: 42 Cov.: 31 AF XY: 0.0125 AC XY: 932AN XY: 74286
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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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