rs981579

Variant summary

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

The ENST00000509416.1(ENSG00000250064):​n.403-34311A>G 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 0.24 in 151,962 control chromosomes in the GnomAD database, including 5,369 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 0.24 ( 5369 hom., cov: 32)

Consequence


ENST00000509416.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104
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 (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC105374557XR_001741640.2 linkuse as main transcriptn.891-34311A>G intron_variant, non_coding_transcript_variant
LOC105374558XR_925528.3 linkuse as main transcriptn.332-20449T>C intron_variant, non_coding_transcript_variant
LOC105374557XR_001741639.2 linkuse as main transcriptn.301-34311A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENST00000509416.1 linkuse as main transcriptn.403-34311A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36494
AN:
151844
Hom.:
5360
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0784
Gnomad AMI
AF:
0.191
Gnomad AMR
AF:
0.357
Gnomad ASJ
AF:
0.331
Gnomad EAS
AF:
0.555
Gnomad SAS
AF:
0.390
Gnomad FIN
AF:
0.257
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.271
Gnomad OTH
AF:
0.259
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.240
AC:
36521
AN:
151962
Hom.:
5369
Cov.:
32
AF XY:
0.244
AC XY:
18092
AN XY:
74264
show subpopulations
Gnomad4 AFR
AF:
0.0784
Gnomad4 AMR
AF:
0.358
Gnomad4 ASJ
AF:
0.331
Gnomad4 EAS
AF:
0.555
Gnomad4 SAS
AF:
0.388
Gnomad4 FIN
AF:
0.257
Gnomad4 NFE
AF:
0.271
Gnomad4 OTH
AF:
0.264
Alfa
AF:
0.266
Hom.:
1048
Bravo
AF:
0.241
Asia WGS
AF:
0.470
AC:
1629
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.1
DANN
Benign
0.45

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: rs981579; hg19: chr4-28545227; API