rs7973719

Variant summary

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

The ENST00000543061.1(ENSG00000255572):​n.324+6529G>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 0.425 in 151,972 control chromosomes in the GnomAD database, including 15,649 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 0.42 ( 15649 hom., cov: 31)

Consequence


ENST00000543061.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.25
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=-1.06).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 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
ENST00000543061.1 linkuse as main transcriptn.324+6529G>A intron_variant, non_coding_transcript_variant 2
ENST00000545794.1 linkuse as main transcriptn.279+6529G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64516
AN:
151854
Hom.:
15639
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.188
Gnomad AMI
AF:
0.632
Gnomad AMR
AF:
0.598
Gnomad ASJ
AF:
0.483
Gnomad EAS
AF:
0.382
Gnomad SAS
AF:
0.469
Gnomad FIN
AF:
0.442
Gnomad MID
AF:
0.497
Gnomad NFE
AF:
0.521
Gnomad OTH
AF:
0.468
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.425
AC:
64528
AN:
151972
Hom.:
15649
Cov.:
31
AF XY:
0.425
AC XY:
31542
AN XY:
74254
show subpopulations
Gnomad4 AFR
AF:
0.187
Gnomad4 AMR
AF:
0.598
Gnomad4 ASJ
AF:
0.483
Gnomad4 EAS
AF:
0.383
Gnomad4 SAS
AF:
0.469
Gnomad4 FIN
AF:
0.442
Gnomad4 NFE
AF:
0.520
Gnomad4 OTH
AF:
0.465
Alfa
AF:
0.470
Hom.:
2198
Bravo
AF:
0.427
Asia WGS
AF:
0.413
AC:
1435
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.36
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: rs7973719; hg19: chr12-7334813; API