GeneBe

rs2415438

Positions:

Variant summary

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

The variant allele was found at a frequency of 0.678 in 152,020 control chromosomes in the GnomAD database, including 36,159 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 0.68 ( 36159 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.212
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.38108328A>G intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000259048ENST00000554687.1 linkuse as main transcriptn.200+60012T>C intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.678
AC:
102928
AN:
151902
Hom.:
36114
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.860
Gnomad AMI
AF:
0.640
Gnomad AMR
AF:
0.662
Gnomad ASJ
AF:
0.611
Gnomad EAS
AF:
0.390
Gnomad SAS
AF:
0.570
Gnomad FIN
AF:
0.577
Gnomad MID
AF:
0.642
Gnomad NFE
AF:
0.620
Gnomad OTH
AF:
0.667
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.678
AC:
103029
AN:
152020
Hom.:
36159
Cov.:
32
AF XY:
0.674
AC XY:
50065
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.860
Gnomad4 AMR
AF:
0.662
Gnomad4 ASJ
AF:
0.611
Gnomad4 EAS
AF:
0.390
Gnomad4 SAS
AF:
0.569
Gnomad4 FIN
AF:
0.577
Gnomad4 NFE
AF:
0.620
Gnomad4 OTH
AF:
0.663
Alfa
AF:
0.618
Hom.:
57111
Bravo
AF:
0.690
Asia WGS
AF:
0.511
AC:
1770
AN:
3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
3.0
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: rs2415438; hg19: chr14-38577533; API