rs9956150

Variant summary

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

The ENST00000580366.1(ENSG00000263765):​n.28-13607G>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 0.853 in 152,214 control chromosomes in the GnomAD database, including 58,715 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 0.85 ( 58715 hom., cov: 32)

Consequence


ENST00000580366.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.307
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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105372058XR_001753390.2 linkuse as main transcriptn.1239-1279G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000580366.1 linkuse as main transcriptn.28-13607G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.854
AC:
129855
AN:
152096
Hom.:
58716
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.521
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.935
Gnomad ASJ
AF:
0.994
Gnomad EAS
AF:
0.996
Gnomad SAS
AF:
0.992
Gnomad FIN
AF:
0.970
Gnomad MID
AF:
0.946
Gnomad NFE
AF:
0.988
Gnomad OTH
AF:
0.892
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.853
AC:
129894
AN:
152214
Hom.:
58715
Cov.:
32
AF XY:
0.857
AC XY:
63803
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.521
Gnomad4 AMR
AF:
0.935
Gnomad4 ASJ
AF:
0.994
Gnomad4 EAS
AF:
0.996
Gnomad4 SAS
AF:
0.992
Gnomad4 FIN
AF:
0.970
Gnomad4 NFE
AF:
0.988
Gnomad4 OTH
AF:
0.891
Alfa
AF:
0.909
Hom.:
8078
Bravo
AF:
0.835
Asia WGS
AF:
0.958
AC:
3328
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.93
DANN
Benign
0.43

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: rs9956150; hg19: chr18-30479190; API