rs1031507

Variant summary

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

The ENST00000623836.1(ENSG00000280083):​n.179T>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 0.566 in 152,100 control chromosomes in the GnomAD database, including 25,972 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 0.57 ( 25970 hom., cov: 32)
Exomes 𝑓: 0.44 ( 2 hom. )

Consequence

ENSG00000280083
ENST00000623836.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.902
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=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 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
ENSG00000280083ENST00000623836.1 linkn.179T>G non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.566
AC:
86086
AN:
151964
Hom.:
25953
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.356
Gnomad AMI
AF:
0.832
Gnomad AMR
AF:
0.659
Gnomad ASJ
AF:
0.641
Gnomad EAS
AF:
0.420
Gnomad SAS
AF:
0.683
Gnomad FIN
AF:
0.643
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.658
Gnomad OTH
AF:
0.564
GnomAD4 exome
AF:
0.444
AC:
8
AN:
18
Hom.:
2
Cov.:
0
AF XY:
0.500
AC XY:
6
AN XY:
12
show subpopulations
Gnomad4 EAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.500
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.566
AC:
86148
AN:
152082
Hom.:
25970
Cov.:
32
AF XY:
0.572
AC XY:
42524
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.356
Gnomad4 AMR
AF:
0.660
Gnomad4 ASJ
AF:
0.641
Gnomad4 EAS
AF:
0.422
Gnomad4 SAS
AF:
0.682
Gnomad4 FIN
AF:
0.643
Gnomad4 NFE
AF:
0.658
Gnomad4 OTH
AF:
0.561
Alfa
AF:
0.621
Hom.:
3849
Bravo
AF:
0.556
Asia WGS
AF:
0.543
AC:
1885
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.4
DANN
Benign
0.72

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: rs1031507; hg19: chr2-192020618; API