rs497387

Variant summary

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

The ENST00000419001.1(SALL4P5):​n.1027A>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 0.558 in 169,924 control chromosomes in the GnomAD database, including 27,125 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 0.53 ( 22105 hom., cov: 35)
Exomes 𝑓: 0.76 ( 5020 hom. )

Consequence

SALL4P5
ENST00000419001.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.402
Variant links:
Genes affected
SALL4P5 (HGNC:39822): (spalt like transcription factor 4 pseudogene 5)

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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SALL4P5ENST00000419001.1 linkuse as main transcriptn.1027A>G non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.534
AC:
81155
AN:
152088
Hom.:
22079
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.604
Gnomad AMI
AF:
0.393
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.520
Gnomad EAS
AF:
0.272
Gnomad SAS
AF:
0.471
Gnomad FIN
AF:
0.509
Gnomad MID
AF:
0.481
Gnomad NFE
AF:
0.523
Gnomad OTH
AF:
0.524
GnomAD4 exome
AF:
0.763
AC:
13519
AN:
17716
Hom.:
5020
Cov.:
0
AF XY:
0.760
AC XY:
6956
AN XY:
9148
show subpopulations
Gnomad4 AFR exome
AF:
0.836
Gnomad4 AMR exome
AF:
0.791
Gnomad4 ASJ exome
AF:
0.712
Gnomad4 EAS exome
AF:
0.640
Gnomad4 SAS exome
AF:
0.773
Gnomad4 FIN exome
AF:
0.744
Gnomad4 NFE exome
AF:
0.762
Gnomad4 OTH exome
AF:
0.754
GnomAD4 genome
AF:
0.534
AC:
81225
AN:
152208
Hom.:
22105
Cov.:
35
AF XY:
0.530
AC XY:
39429
AN XY:
74420
show subpopulations
Gnomad4 AFR
AF:
0.604
Gnomad4 AMR
AF:
0.529
Gnomad4 ASJ
AF:
0.520
Gnomad4 EAS
AF:
0.271
Gnomad4 SAS
AF:
0.469
Gnomad4 FIN
AF:
0.509
Gnomad4 NFE
AF:
0.523
Gnomad4 OTH
AF:
0.524
Alfa
AF:
0.525
Hom.:
12413
Bravo
AF:
0.541
Asia WGS
AF:
0.425
AC:
1481
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.96
DANN
Benign
0.077

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: rs497387; hg19: chr3-23032340; API