rs7233739

Variant summary

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

The ENST00000623844.1(ENSG00000279479):​n.1437G>A 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 0.533 in 152,072 control chromosomes in the GnomAD database, including 21,864 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 0.53 ( 21864 hom., cov: 33)
Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

ENSG00000279479
ENST00000623844.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000279479ENST00000623844.1 linkn.1437G>A non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.533
AC:
81027
AN:
151948
Hom.:
21822
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.540
Gnomad AMI
AF:
0.651
Gnomad AMR
AF:
0.566
Gnomad ASJ
AF:
0.587
Gnomad EAS
AF:
0.453
Gnomad SAS
AF:
0.708
Gnomad FIN
AF:
0.496
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.517
Gnomad OTH
AF:
0.532
GnomAD4 exome
AF:
0.333
AC:
2
AN:
6
Hom.:
0
Cov.:
0
AF XY:
0.500
AC XY:
1
AN XY:
2
show subpopulations
Gnomad4 FIN exome
AF:
0.333
GnomAD4 genome
AF:
0.533
AC:
81124
AN:
152066
Hom.:
21864
Cov.:
33
AF XY:
0.536
AC XY:
39849
AN XY:
74332
show subpopulations
Gnomad4 AFR
AF:
0.541
Gnomad4 AMR
AF:
0.566
Gnomad4 ASJ
AF:
0.587
Gnomad4 EAS
AF:
0.452
Gnomad4 SAS
AF:
0.708
Gnomad4 FIN
AF:
0.496
Gnomad4 NFE
AF:
0.517
Gnomad4 OTH
AF:
0.530
Alfa
AF:
0.533
Hom.:
3656
Bravo
AF:
0.534
Asia WGS
AF:
0.583
AC:
2029
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.32
DANN
Benign
0.61

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: rs7233739; hg19: chr18-6728488; API