rs1074651

Variant summary

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

The ENST00000561657.1(ENSG00000261028):​n.381+4821A>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 0.369 in 152,008 control chromosomes in the GnomAD database, including 10,756 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 0.37 ( 10756 hom., cov: 32)

Consequence


ENST00000561657.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000561657.1 linkuse as main transcriptn.381+4821A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.369
AC:
56070
AN:
151888
Hom.:
10740
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.451
Gnomad AMI
AF:
0.438
Gnomad AMR
AF:
0.412
Gnomad ASJ
AF:
0.373
Gnomad EAS
AF:
0.348
Gnomad SAS
AF:
0.241
Gnomad FIN
AF:
0.353
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.323
Gnomad OTH
AF:
0.342
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.369
AC:
56128
AN:
152008
Hom.:
10756
Cov.:
32
AF XY:
0.369
AC XY:
27401
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.451
Gnomad4 AMR
AF:
0.412
Gnomad4 ASJ
AF:
0.373
Gnomad4 EAS
AF:
0.348
Gnomad4 SAS
AF:
0.241
Gnomad4 FIN
AF:
0.353
Gnomad4 NFE
AF:
0.323
Gnomad4 OTH
AF:
0.339
Alfa
AF:
0.333
Hom.:
3960
Bravo
AF:
0.380
Asia WGS
AF:
0.323
AC:
1126
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.35
DANN
Benign
0.66

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: rs1074651; hg19: chr16-64372612; API