rs109889

Variant summary

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

The ENST00000668438.1(ENSG00000287451):​n.467-15828G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,046 control chromosomes in the GnomAD database, including 13,556 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 0.39 ( 13556 hom., cov: 32)

Consequence

ENSG00000287451
ENST00000668438.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395
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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000287451ENST00000668438.1 linkn.467-15828G>C intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.387
AC:
58792
AN:
151928
Hom.:
13553
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.316
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.487
Gnomad EAS
AF:
0.171
Gnomad SAS
AF:
0.443
Gnomad FIN
AF:
0.550
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.489
Gnomad OTH
AF:
0.417
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.387
AC:
58812
AN:
152046
Hom.:
13556
Cov.:
32
AF XY:
0.389
AC XY:
28928
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.148
Gnomad4 AMR
AF:
0.503
Gnomad4 ASJ
AF:
0.487
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.441
Gnomad4 FIN
AF:
0.550
Gnomad4 NFE
AF:
0.489
Gnomad4 OTH
AF:
0.415
Alfa
AF:
0.432
Hom.:
1929
Bravo
AF:
0.370
Asia WGS
AF:
0.309
AC:
1075
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.7
DANN
Benign
0.57

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: rs109889; hg19: chr2-116608834; API