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GeneBe

rs10468017

chr15-58386313-C-T

Variant summary

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

The ENST00000558239.5(ALDH1A2):c.-172+33658G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151984 control chromosomes in the gnomAD Genomes database, including 4847 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 0.24 ( 4847 hom., cov: 32)

Consequence

ALDH1A2
ENST00000558239.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.169

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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
ALDH1A2ENST00000558239.5 linkuse as main transcriptc.-172+33658G>A intron_variant 4
ALDH1A2ENST00000560863.5 linkuse as main transcriptn.415+33658G>A intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.241
AC:
36702
AN:
151984
Hom.:
4847
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.162
Gnomad AMI
AF:
0.253
Gnomad AMR
AF:
0.222
Gnomad ASJ
AF:
0.254
Gnomad EAS
AF:
0.188
Gnomad SAS
AF:
0.191
Gnomad FIN
AF:
0.341
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.286
Gnomad OTH
AF:
0.247
Alfa
AF:
0.272
Hom.:
9066
Bravo
AF:
0.228
Asia WGS
AF:
0.214
AC:
746
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
1.7
Dann
Benign
0.84

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: rs10468017; hg19: chr15-58678512;