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GeneBe

rs9315219

Variant summary

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

The ENST00000686875.1(null):n.278+35591G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,102 control chromosomes in the GnomAD database, including 6,289 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 0.26 ( 6289 hom., cov: 32)

Consequence


ENST00000686875.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.432
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 (NFE) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STARD13NM_001243476.3 linkuse as main transcriptc.30+35591G>A intron_variant
STARD13XM_017020835.3 linkuse as main transcriptc.30+35591G>A intron_variant
STARD13XM_024449429.2 linkuse as main transcriptc.30+35591G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000686875.1 linkuse as main transcriptn.278+35591G>A intron_variant, non_coding_transcript_variant
ENST00000454681.2 linkuse as main transcriptn.226+35591G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.260
AC:
39456
AN:
151984
Hom.:
6289
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0749
Gnomad AMI
AF:
0.337
Gnomad AMR
AF:
0.287
Gnomad ASJ
AF:
0.265
Gnomad EAS
AF:
0.208
Gnomad SAS
AF:
0.314
Gnomad FIN
AF:
0.296
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.359
Gnomad OTH
AF:
0.277
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.259
AC:
39451
AN:
152102
Hom.:
6289
Cov.:
32
AF XY:
0.257
AC XY:
19095
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0747
Gnomad4 AMR
AF:
0.286
Gnomad4 ASJ
AF:
0.265
Gnomad4 EAS
AF:
0.208
Gnomad4 SAS
AF:
0.314
Gnomad4 FIN
AF:
0.296
Gnomad4 NFE
AF:
0.359
Gnomad4 OTH
AF:
0.274
Alfa
AF:
0.302
Hom.:
1017
Bravo
AF:
0.251
Asia WGS
AF:
0.237
AC:
822
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
1.1
Dann
Benign
0.64

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: rs9315219; hg19: chr13-34062784; API