rs2179652

Variant summary

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

The ENST00000429211.2(ENSG00000226814):​n.126C>T 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 0.559 in 206,522 control chromosomes in the GnomAD database, including 32,369 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 0.56 ( 23688 hom., cov: 30)
Exomes 𝑓: 0.57 ( 8681 hom. )

Consequence


ENST00000429211.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.45
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=-0.61).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000429211.2 linkuse as main transcriptn.126C>T non_coding_transcript_exon_variant 1/1
ENST00000644134.1 linkuse as main transcriptn.105-34502G>A intron_variant, non_coding_transcript_variant
ENST00000644058.1 linkuse as main transcriptn.194-34502G>A intron_variant, non_coding_transcript_variant
ENST00000645822.1 linkuse as main transcriptn.200-8228G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84303
AN:
151642
Hom.:
23662
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.620
Gnomad AMI
AF:
0.678
Gnomad AMR
AF:
0.529
Gnomad ASJ
AF:
0.607
Gnomad EAS
AF:
0.630
Gnomad SAS
AF:
0.607
Gnomad FIN
AF:
0.413
Gnomad MID
AF:
0.611
Gnomad NFE
AF:
0.532
Gnomad OTH
AF:
0.553
GnomAD4 exome
AF:
0.568
AC:
31098
AN:
54762
Hom.:
8681
Cov.:
0
AF XY:
0.571
AC XY:
18458
AN XY:
32344
show subpopulations
Gnomad4 AFR exome
AF:
0.644
Gnomad4 AMR exome
AF:
0.506
Gnomad4 ASJ exome
AF:
0.636
Gnomad4 EAS exome
AF:
0.657
Gnomad4 SAS exome
AF:
0.627
Gnomad4 FIN exome
AF:
0.478
Gnomad4 NFE exome
AF:
0.565
Gnomad4 OTH exome
AF:
0.547
GnomAD4 genome
AF:
0.556
AC:
84375
AN:
151760
Hom.:
23688
Cov.:
30
AF XY:
0.553
AC XY:
40979
AN XY:
74132
show subpopulations
Gnomad4 AFR
AF:
0.620
Gnomad4 AMR
AF:
0.528
Gnomad4 ASJ
AF:
0.607
Gnomad4 EAS
AF:
0.630
Gnomad4 SAS
AF:
0.606
Gnomad4 FIN
AF:
0.413
Gnomad4 NFE
AF:
0.532
Gnomad4 OTH
AF:
0.554
Alfa
AF:
0.547
Hom.:
3300
Bravo
AF:
0.563
Asia WGS
AF:
0.644
AC:
2236
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.61
CADD
Benign
1.9
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: rs2179652; hg19: chr1-192769826; API