rs7001413

Variant summary

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

The ENST00000519323.1(ENSG00000254288):​n.304-1421G>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 0.0551 in 152,170 control chromosomes in the GnomAD database, including 413 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 0.055 ( 413 hom., cov: 32)

Consequence


ENST00000519323.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.131
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LY96XM_017013299.2 linkuse as main transcriptc.385-1421G>T intron_variant
LY96XM_017013300.2 linkuse as main transcriptc.295-1421G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000519323.1 linkuse as main transcriptn.304-1421G>T intron_variant, non_coding_transcript_variant 1
ENST00000668834.1 linkuse as main transcriptn.175+4279G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0549
AC:
8347
AN:
152052
Hom.:
405
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.129
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0425
Gnomad ASJ
AF:
0.0409
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00767
Gnomad FIN
AF:
0.0375
Gnomad MID
AF:
0.0316
Gnomad NFE
AF:
0.0239
Gnomad OTH
AF:
0.0602
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0551
AC:
8384
AN:
152170
Hom.:
413
Cov.:
32
AF XY:
0.0532
AC XY:
3957
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.0423
Gnomad4 ASJ
AF:
0.0409
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00768
Gnomad4 FIN
AF:
0.0375
Gnomad4 NFE
AF:
0.0239
Gnomad4 OTH
AF:
0.0643
Alfa
AF:
0.0309
Hom.:
105
Bravo
AF:
0.0588
Asia WGS
AF:
0.0290
AC:
99
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
3.0
DANN
Benign
0.34

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: rs7001413; hg19: chr8-75010233; API