GeneBe

rs1635135

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 0.222 in 152,018 control chromosomes in the GnomAD database, including 4,222 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 0.22 ( 4222 hom., cov: 32)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.792
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.113017091A>G intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000257452ENST00000552784.1 linkuse as main transcriptn.353+308T>C intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.222
AC:
33707
AN:
151900
Hom.:
4224
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.0493
Gnomad AMR
AF:
0.232
Gnomad ASJ
AF:
0.164
Gnomad EAS
AF:
0.477
Gnomad SAS
AF:
0.331
Gnomad FIN
AF:
0.318
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.242
Gnomad OTH
AF:
0.222
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.222
AC:
33716
AN:
152018
Hom.:
4222
Cov.:
32
AF XY:
0.228
AC XY:
16941
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.232
Gnomad4 ASJ
AF:
0.164
Gnomad4 EAS
AF:
0.477
Gnomad4 SAS
AF:
0.330
Gnomad4 FIN
AF:
0.318
Gnomad4 NFE
AF:
0.243
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.239
Hom.:
2451
Bravo
AF:
0.212
Asia WGS
AF:
0.372
AC:
1290
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.1
DANN
Benign
0.49

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: rs1635135; hg19: chr12-113454896; API