rs4968779

Variant summary

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

The ENST00000582741.1(ENSG00000265971):​n.218A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,112 control chromosomes in the GnomAD database, including 26,662 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 0.58 ( 26660 hom., cov: 32)
Exomes 𝑓: 0.64 ( 2 hom. )

Consequence


ENST00000582741.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.317
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 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
ENST00000582741.1 linkuse as main transcriptn.218A>G non_coding_transcript_exon_variant 1/24

Frequencies

GnomAD3 genomes
AF:
0.575
AC:
87447
AN:
151980
Hom.:
26610
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.770
Gnomad AMI
AF:
0.596
Gnomad AMR
AF:
0.464
Gnomad ASJ
AF:
0.494
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.518
Gnomad FIN
AF:
0.556
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.525
Gnomad OTH
AF:
0.524
GnomAD4 exome
AF:
0.643
AC:
9
AN:
14
Hom.:
2
Cov.:
0
AF XY:
0.625
AC XY:
5
AN XY:
8
show subpopulations
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.833
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.576
AC:
87557
AN:
152098
Hom.:
26660
Cov.:
32
AF XY:
0.570
AC XY:
42373
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.771
Gnomad4 AMR
AF:
0.464
Gnomad4 ASJ
AF:
0.494
Gnomad4 EAS
AF:
0.176
Gnomad4 SAS
AF:
0.518
Gnomad4 FIN
AF:
0.556
Gnomad4 NFE
AF:
0.525
Gnomad4 OTH
AF:
0.529
Alfa
AF:
0.519
Hom.:
25184
Bravo
AF:
0.572
Asia WGS
AF:
0.418
AC:
1453
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.98
DANN
Benign
0.47

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: rs4968779; hg19: chr17-61532571; API