rs730570

Variant summary

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

The ENST00000557546.1(ENSG00000258717):​n.104-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,896 control chromosomes in the GnomAD database, including 36,782 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 0.65 ( 36520 hom., cov: 31)
Exomes 𝑓: 0.73 ( 262 hom. )

Consequence

ENSG00000258717
ENST00000557546.1 splice_region, intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.37
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=-0.81).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 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
ENSG00000258717ENST00000557546.1 linkn.104-5C>T splice_region_variant, intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.647
AC:
98248
AN:
151876
Hom.:
36527
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.329
Gnomad AMI
AF:
0.868
Gnomad AMR
AF:
0.550
Gnomad ASJ
AF:
0.852
Gnomad EAS
AF:
0.212
Gnomad SAS
AF:
0.587
Gnomad FIN
AF:
0.776
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.863
Gnomad OTH
AF:
0.687
GnomAD4 exome
AF:
0.733
AC:
661
AN:
902
Hom.:
262
Cov.:
0
AF XY:
0.732
AC XY:
376
AN XY:
514
show subpopulations
Gnomad4 AFR exome
AF:
0.300
Gnomad4 AMR exome
AF:
0.700
Gnomad4 ASJ exome
AF:
0.813
Gnomad4 EAS exome
AF:
0.127
Gnomad4 SAS exome
AF:
0.583
Gnomad4 FIN exome
AF:
0.745
Gnomad4 NFE exome
AF:
0.854
Gnomad4 OTH exome
AF:
0.688
GnomAD4 genome
AF:
0.646
AC:
98246
AN:
151994
Hom.:
36520
Cov.:
31
AF XY:
0.636
AC XY:
47251
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.329
Gnomad4 AMR
AF:
0.549
Gnomad4 ASJ
AF:
0.852
Gnomad4 EAS
AF:
0.211
Gnomad4 SAS
AF:
0.588
Gnomad4 FIN
AF:
0.776
Gnomad4 NFE
AF:
0.863
Gnomad4 OTH
AF:
0.679
Alfa
AF:
0.824
Hom.:
81139
Bravo
AF:
0.614
Asia WGS
AF:
0.350
AC:
1220
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.2
DANN
Benign
0.67

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: rs730570; hg19: chr14-101142890; API