rs2097937

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 0.733 in 207,796 control chromosomes in the GnomAD database, including 57,797 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 0.71 ( 40063 hom., cov: 32)
Exomes 𝑓: 0.80 ( 17734 hom. )

Consequence


intergenic_region

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.167
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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.87401587G>A intergenic_region
ABCB4XR_007060045.1 linkuse as main transcriptn.4237+246C>T intron_variant
ABCB4XR_007060046.1 linkuse as main transcriptn.4132+246C>T intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.711
AC:
108024
AN:
151922
Hom.:
40067
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.476
Gnomad AMI
AF:
0.860
Gnomad AMR
AF:
0.783
Gnomad ASJ
AF:
0.807
Gnomad EAS
AF:
0.700
Gnomad SAS
AF:
0.729
Gnomad FIN
AF:
0.792
Gnomad MID
AF:
0.832
Gnomad NFE
AF:
0.816
Gnomad OTH
AF:
0.756
GnomAD4 exome
AF:
0.795
AC:
44329
AN:
55754
Hom.:
17734
AF XY:
0.793
AC XY:
23367
AN XY:
29464
show subpopulations
Gnomad4 AFR exome
AF:
0.494
Gnomad4 AMR exome
AF:
0.723
Gnomad4 ASJ exome
AF:
0.847
Gnomad4 EAS exome
AF:
0.708
Gnomad4 SAS exome
AF:
0.752
Gnomad4 FIN exome
AF:
0.808
Gnomad4 NFE exome
AF:
0.828
Gnomad4 OTH exome
AF:
0.784
GnomAD4 genome
AF:
0.711
AC:
108048
AN:
152042
Hom.:
40063
Cov.:
32
AF XY:
0.712
AC XY:
52911
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.476
Gnomad4 AMR
AF:
0.783
Gnomad4 ASJ
AF:
0.807
Gnomad4 EAS
AF:
0.701
Gnomad4 SAS
AF:
0.728
Gnomad4 FIN
AF:
0.792
Gnomad4 NFE
AF:
0.816
Gnomad4 OTH
AF:
0.751
Alfa
AF:
0.793
Hom.:
67944
Bravo
AF:
0.699
Asia WGS
AF:
0.707
AC:
2453
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.84
DANN
Benign
0.41

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: rs2097937; hg19: chr7-87030903; API