rs6945541

Variant summary

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

The ENST00000661243.1(ENSG00000286466):​n.1354-847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,062 control chromosomes in the GnomAD database, including 36,735 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 ( 36735 hom., cov: 33)

Consequence

ENSG00000286466
ENST00000661243.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105375343XR_927647.1 linkuse as main transcriptn.88-847G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000286466ENST00000661243.1 linkuse as main transcriptn.1354-847G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.679
AC:
103127
AN:
151944
Hom.:
36681
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.877
Gnomad AMI
AF:
0.663
Gnomad AMR
AF:
0.672
Gnomad ASJ
AF:
0.512
Gnomad EAS
AF:
0.970
Gnomad SAS
AF:
0.736
Gnomad FIN
AF:
0.627
Gnomad MID
AF:
0.595
Gnomad NFE
AF:
0.552
Gnomad OTH
AF:
0.638
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.679
AC:
103240
AN:
152062
Hom.:
36735
Cov.:
33
AF XY:
0.685
AC XY:
50916
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.877
Gnomad4 AMR
AF:
0.672
Gnomad4 ASJ
AF:
0.512
Gnomad4 EAS
AF:
0.970
Gnomad4 SAS
AF:
0.735
Gnomad4 FIN
AF:
0.627
Gnomad4 NFE
AF:
0.551
Gnomad4 OTH
AF:
0.639
Alfa
AF:
0.613
Hom.:
11808
Bravo
AF:
0.692
Asia WGS
AF:
0.837
AC:
2905
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.74
DANN
Benign
0.76

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: rs6945541; hg19: chr7-68611960; API