rs1290349

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000527589.1(ENSG00000254638):​n.171-655G>T 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 0.253 in 152,068 control chromosomes in the GnomAD database, including 5,045 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.25 ( 5045 hom., cov: 32)

Consequence


ENST00000527589.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.264
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 11-112166831-C-A is Benign according to our data. Variant chr11-112166831-C-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107987164XR_001748384.2 linkuse as main transcriptn.81+232G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000527589.1 linkuse as main transcriptn.171-655G>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.253
AC:
38427
AN:
151952
Hom.:
5046
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.214
Gnomad AMI
AF:
0.237
Gnomad AMR
AF:
0.298
Gnomad ASJ
AF:
0.267
Gnomad EAS
AF:
0.128
Gnomad SAS
AF:
0.217
Gnomad FIN
AF:
0.287
Gnomad MID
AF:
0.269
Gnomad NFE
AF:
0.273
Gnomad OTH
AF:
0.248
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.253
AC:
38420
AN:
152068
Hom.:
5045
Cov.:
32
AF XY:
0.253
AC XY:
18800
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.214
Gnomad4 AMR
AF:
0.298
Gnomad4 ASJ
AF:
0.267
Gnomad4 EAS
AF:
0.128
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.287
Gnomad4 NFE
AF:
0.272
Gnomad4 OTH
AF:
0.245
Alfa
AF:
0.269
Hom.:
5347
Bravo
AF:
0.253
Asia WGS
AF:
0.186
AC:
647
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.3
DANN
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs1290349; hg19: chr11-112037554; API