rs181651384

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_003240.5(LEFTY2):​c.330C>T​(p.Asn110Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000584 in 1,585,144 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0032 ( 4 hom., cov: 33)
Exomes 𝑓: 0.00031 ( 2 hom. )

Consequence

LEFTY2
NM_003240.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.57
Variant links:
Genes affected
LEFTY2 (HGNC:3122): (left-right determination factor 2) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate the mature protein, which plays a role in left-right asymmetry determination of organ systems during development. The protein may also play a role in endometrial bleeding. Mutations in this gene have been associated with left-right axis malformations, particularly in the heart and lungs. Some types of infertility have been associated with dysregulated expression of this gene in the endometrium. This gene is closely linked to both a related family member and a related pseudogene. This gene encodes multiple isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Aug 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 1-225939923-G-A is Benign according to our data. Variant chr1-225939923-G-A is described in ClinVar as [Benign]. Clinvar id is 239525.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.57 with no splicing effect.
BS2
High AC in GnomAd4 at 485 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LEFTY2NM_003240.5 linkuse as main transcriptc.330C>T p.Asn110Asn synonymous_variant 2/4 ENST00000366820.10 NP_003231.2 O00292-1A1NY82
LEFTY2XM_011544266.2 linkuse as main transcriptc.330C>T p.Asn110Asn synonymous_variant 2/4 XP_011542568.1
LEFTY2NM_001172425.3 linkuse as main transcriptc.279+51C>T intron_variant NP_001165896.1 O00292-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LEFTY2ENST00000366820.10 linkuse as main transcriptc.330C>T p.Asn110Asn synonymous_variant 2/41 NM_003240.5 ENSP00000355785.5 O00292-1
LEFTY2ENST00000420304.6 linkuse as main transcriptc.279+51C>T intron_variant 2 ENSP00000388009.2 O00292-2
LEFTY2ENST00000474493.1 linkuse as main transcriptn.179C>T non_coding_transcript_exon_variant 1/23

Frequencies

GnomAD3 genomes
AF:
0.00316
AC:
481
AN:
152268
Hom.:
4
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0110
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00131
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:
0.0000147
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.000688
AC:
135
AN:
196106
Hom.:
1
AF XY:
0.000569
AC XY:
62
AN XY:
108982
show subpopulations
Gnomad AFR exome
AF:
0.0112
Gnomad AMR exome
AF:
0.000162
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000229
Gnomad OTH exome
AF:
0.000395
GnomAD4 exome
AF:
0.000308
AC:
441
AN:
1432758
Hom.:
2
Cov.:
34
AF XY:
0.000272
AC XY:
194
AN XY:
712040
show subpopulations
Gnomad4 AFR exome
AF:
0.0117
Gnomad4 AMR exome
AF:
0.000211
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000254
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000361
Gnomad4 OTH exome
AF:
0.000587
GnomAD4 genome
AF:
0.00318
AC:
485
AN:
152386
Hom.:
4
Cov.:
33
AF XY:
0.00306
AC XY:
228
AN XY:
74516
show subpopulations
Gnomad4 AFR
AF:
0.0111
Gnomad4 AMR
AF:
0.00124
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00141
Hom.:
0
Bravo
AF:
0.00338

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Left-right axis malformations Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 21, 2023- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
7.7
DANN
Benign
0.97

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: rs181651384; hg19: chr1-226127623; API