rs2317951

Variant summary

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

The ENST00000689429.1(ENSG00000242396):​n.325-4673G>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 0.315 in 152,042 control chromosomes in the GnomAD database, including 7,717 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 0.31 ( 7717 hom., cov: 32)

Consequence


ENST00000689429.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580
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=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124904184XR_007066103.1 linkuse as main transcriptn.133-4673G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000689429.1 linkuse as main transcriptn.325-4673G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.315
AC:
47817
AN:
151924
Hom.:
7722
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.288
Gnomad AMI
AF:
0.349
Gnomad AMR
AF:
0.268
Gnomad ASJ
AF:
0.405
Gnomad EAS
AF:
0.132
Gnomad SAS
AF:
0.294
Gnomad FIN
AF:
0.350
Gnomad MID
AF:
0.459
Gnomad NFE
AF:
0.346
Gnomad OTH
AF:
0.316
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.315
AC:
47835
AN:
152042
Hom.:
7717
Cov.:
32
AF XY:
0.313
AC XY:
23232
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.268
Gnomad4 ASJ
AF:
0.405
Gnomad4 EAS
AF:
0.132
Gnomad4 SAS
AF:
0.295
Gnomad4 FIN
AF:
0.350
Gnomad4 NFE
AF:
0.346
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.340
Hom.:
18166
Bravo
AF:
0.305
Asia WGS
AF:
0.230
AC:
797
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.9
DANN
Benign
0.51

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: rs2317951; hg19: chr1-55434648; API