dbSNP rs4459845: ALDH1L1-AS2:n.482-9541A>C (chr3-126198785-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000500232.3(ALDH1L1-AS2):n.482-9541A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,194 control chromosomes in the GnomAD database, including 2,607 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 0.18 ( 2607 hom., cov: 33)

Consequence

ALDH1L1-AS2
ENST00000500232.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.261

Publications

3 publications found

Variant links:

Genes affected

ALDH1L1-AS2 (HGNC:42446): (ALDH1L1 antisense RNA 2)

ALDH1L1-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1L1-AS2	NR_046383.1 link	n.481-9541A>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ALDH1L1-AS2	ENST00000500232.3 link	n.482-9541A>C	intron_variant	Intron 1 of 1	1
ALDH1L1-AS2	ENST00000502278.2 link	n.291-9541A>C	intron_variant	Intron 1 of 1	4
ALDH1L1-AS2	ENST00000654154.2 link	n.534-9541A>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27586

AN:

152078

Hom.:

2612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.0804

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.196

Gnomad OTH

AF:

0.195

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.181

AC:

27588

AN:

152194

Hom.:

2607

Cov.:

AF XY:

0.180

AC XY:

13392

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.180

AC:

7473

AN:

41522

American (AMR)

AF:

0.138

AC:

2114

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

748

AN:

3468

East Asian (EAS)

AF:

0.0800

AC:

414

AN:

5174

South Asian (SAS)

AF:

0.214

AC:

1032

AN:

4822

European-Finnish (FIN)

AF:

0.174

AC:

1844

AN:

10592

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.196

AC:

13338

AN:

68002

Other (OTH)

AF:

0.193

AC:

407

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1130

2260

3391

4521

5651

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.184

Hom.:

326

Bravo

AF:

0.176

Asia WGS

AF:

0.154

AC:

538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.1

(source)

DANN

Benign

0.50

PhyloP100

0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over