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GeneBe

17-64860033-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_199340.5(LRRC37A3):c.4113T>C(p.Pro1371=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00277 in 1,613,970 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 51 hom., cov: 31)
Exomes 𝑓: 0.0015 ( 50 hom. )

Consequence

LRRC37A3
NM_199340.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0810
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-64860033-A-G is Benign according to our data. Variant chr17-64860033-A-G is described in ClinVar as [Benign]. Clinvar id is 768909.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.081 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0525 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRRC37A3NM_199340.5 linkuse as main transcriptc.4113T>C p.Pro1371= synonymous_variant 12/15 ENST00000584306.6
LOC105376844XR_934912.4 linkuse as main transcriptn.177+10046A>G intron_variant, non_coding_transcript_variant
LRRC37A3NM_001303255.3 linkuse as main transcriptc.1467T>C p.Pro489= synonymous_variant 8/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRRC37A3ENST00000584306.6 linkuse as main transcriptc.4113T>C p.Pro1371= synonymous_variant 12/151 NM_199340.5 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0146
AC:
2221
AN:
152204
Hom.:
51
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0503
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00667
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.0129
GnomAD3 exomes
AF:
0.00385
AC:
958
AN:
248774
Hom.:
27
AF XY:
0.00291
AC XY:
393
AN XY:
135010
show subpopulations
Gnomad AFR exome
AF:
0.0553
Gnomad AMR exome
AF:
0.00289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000623
Gnomad OTH exome
AF:
0.00231
GnomAD4 exome
AF:
0.00153
AC:
2239
AN:
1461648
Hom.:
50
Cov.:
33
AF XY:
0.00127
AC XY:
925
AN XY:
727136
show subpopulations
Gnomad4 AFR exome
AF:
0.0546
Gnomad4 AMR exome
AF:
0.00349
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000104
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000414
Gnomad4 OTH exome
AF:
0.00321
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0146
AC:
2224
AN:
152322
Hom.:
51
Cov.:
31
AF XY:
0.0141
AC XY:
1050
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0502
Gnomad4 AMR
AF:
0.00667
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.0128
Alfa
AF:
0.00724
Hom.:
13
Bravo
AF:
0.0170
Asia WGS
AF:
0.00433
AC:
15
AN:
3478
EpiCase
AF:
0.000109
EpiControl
AF:
0.0000593

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 submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
1.2
Dann
Benign
0.46

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs115281074; hg19: chr17-62856151; API