rs2374459

Variant summary

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

The XM_047446566.1(LOC107985876):​c.*2039C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,054 control chromosomes in the GnomAD database, including 23,364 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 0.54 ( 23364 hom., cov: 32)

Consequence

LOC107985876
XM_047446566.1 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03
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 (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107985876XM_047446566.1 linkuse as main transcriptc.*2039C>T 3_prime_UTR_variant 3/3
LOC107985876XM_017005460.2 linkuse as main transcriptc.*1348C>T 3_prime_UTR_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.536
AC:
81499
AN:
151936
Hom.:
23364
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.336
Gnomad AMI
AF:
0.621
Gnomad AMR
AF:
0.596
Gnomad ASJ
AF:
0.595
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.482
Gnomad FIN
AF:
0.699
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.630
Gnomad OTH
AF:
0.546
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.536
AC:
81524
AN:
152054
Hom.:
23364
Cov.:
32
AF XY:
0.539
AC XY:
40074
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.336
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.595
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.481
Gnomad4 FIN
AF:
0.699
Gnomad4 NFE
AF:
0.630
Gnomad4 OTH
AF:
0.546
Alfa
AF:
0.607
Hom.:
46453
Bravo
AF:
0.521
Asia WGS
AF:
0.435
AC:
1514
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
0.028
DANN
Benign
0.59

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: rs2374459; hg19: chr2-43292832; API