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GeneBe

rs340874

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000610409.1(null):n.507A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,950 control chromosomes in the GnomAD database, including 14,774 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.41 ( 14770 hom., cov: 31)
Exomes 𝑓: 0.56 ( 4 hom. )

Consequence


ENST00000610409.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0990
Variant links:
Genes affected
PROX1-AS1 (HGNC:43656): (PROX1 antisense RNA 1)
PROX1 (HGNC:9459): (prospero homeobox 1) The protein encoded by this gene is a member of the homeobox transcription factor family. Members of this family contain a homeobox domain that consists of a 60-amino acid helix-turn-helix structure that binds DNA and RNA. The protein encoded by this gene is conserved across vertebrates and may play an essential role during development. Altered levels of this protein have been reported in cancers of different organs, such as colon, brain, blood, breast, pancreas, liver and esophagus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PROX1-AS1NR_037850.2 linkuse as main transcriptn.85+156A>G intron_variant, non_coding_transcript_variant
PROX1XM_011509773.3 linkuse as main transcriptc.-68+2590T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000610409.1 linkuse as main transcriptn.507A>G non_coding_transcript_exon_variant 1/1
PROX1-AS1ENST00000433082.6 linkuse as main transcriptn.62+2408A>G intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.410
AC:
62269
AN:
151796
Hom.:
14766
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.166
Gnomad AMI
AF:
0.610
Gnomad AMR
AF:
0.416
Gnomad ASJ
AF:
0.466
Gnomad EAS
AF:
0.398
Gnomad SAS
AF:
0.530
Gnomad FIN
AF:
0.407
Gnomad MID
AF:
0.430
Gnomad NFE
AF:
0.544
Gnomad OTH
AF:
0.439
GnomAD4 exome
AF:
0.556
AC:
20
AN:
36
Hom.:
4
Cov.:
0
AF XY:
0.607
AC XY:
17
AN XY:
28
show subpopulations
Gnomad4 AMR exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.750
Gnomad4 NFE exome
AF:
0.458
Gnomad4 OTH exome
AF:
1.00
GnomAD4 genome
AF:
0.410
AC:
62259
AN:
151914
Hom.:
14770
Cov.:
31
AF XY:
0.405
AC XY:
30041
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.166
Gnomad4 AMR
AF:
0.416
Gnomad4 ASJ
AF:
0.466
Gnomad4 EAS
AF:
0.398
Gnomad4 SAS
AF:
0.530
Gnomad4 FIN
AF:
0.407
Gnomad4 NFE
AF:
0.544
Gnomad4 OTH
AF:
0.437
Alfa
AF:
0.516
Hom.:
35649
Bravo
AF:
0.398
Asia WGS
AF:
0.433
AC:
1505
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
Cadd
Benign
3.9
Dann
Benign
0.77

Splicing

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: rs340874; hg19: chr1-214159256; API