rs2080161

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 0.196 in 149,920 control chromosomes in the GnomAD database, including 3,836 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 0.20 ( 3836 hom., cov: 30)

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.196
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=-0.73).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.13291525A>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000229618ENST00000411542.1 linkuse as main transcriptn.237-18684A>C intron_variant 4
ENSG00000229618ENST00000638964.1 linkuse as main transcriptn.609-18684A>C intron_variant 5
ENSG00000229618ENST00000639998.1 linkuse as main transcriptn.608-18684A>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29409
AN:
149824
Hom.:
3823
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0669
Gnomad AMI
AF:
0.371
Gnomad AMR
AF:
0.400
Gnomad ASJ
AF:
0.174
Gnomad EAS
AF:
0.257
Gnomad SAS
AF:
0.256
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.175
Gnomad NFE
AF:
0.217
Gnomad OTH
AF:
0.202
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29441
AN:
149920
Hom.:
3836
Cov.:
30
AF XY:
0.204
AC XY:
14916
AN XY:
73126
show subpopulations
Gnomad4 AFR
AF:
0.0669
Gnomad4 AMR
AF:
0.401
Gnomad4 ASJ
AF:
0.174
Gnomad4 EAS
AF:
0.258
Gnomad4 SAS
AF:
0.257
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.217
Gnomad4 OTH
AF:
0.202
Alfa
AF:
0.207
Hom.:
4245
Bravo
AF:
0.205
Asia WGS
AF:
0.243
AC:
839
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
0.37
DANN
Benign
0.86

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: rs2080161; hg19: chr7-13331150; API