Genetic Variant ALDH1B1:p.Thr61Thr (chr9-38395931-C-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000692.5(ALDH1B1):c.183C>T(p.Thr61Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,613,694 control chromosomes in the GnomAD database, including 22,051 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2874 hom., cov: 32)

Exomes 𝑓: 0.15 ( 19177 hom. )

Consequence

ALDH1B1
NM_000692.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.91

Variant links:

Genes affected

ALDH1B1 (HGNC:407): (aldehyde dehydrogenase 1 family member B1) This protein belongs to the aldehyde dehydrogenases family of proteins. Aldehyde dehydrogenase is the second enzyme of the major oxidative pathway of alcohol metabolism. This gene does not contain introns in the coding sequence. The variation of this locus may affect the development of alcohol-related problems. [provided by RefSeq, Jul 2008]

ALDH1B1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 9-38395931-C-T is Benign according to our data. Variant chr9-38395931-C-T is described in ClinVar as [Benign]. Clinvar id is 136359.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1B1	NM_000692.5 link	c.183C>T	p.Thr61Thr	synonymous_variant	Exon 2 of 2	ENST00000377698.4	NP_000683.3	P30837A0A384MTJ7
ALDH1B1	XM_011517802.3 link	c.324C>T	p.Thr108Thr	synonymous_variant	Exon 2 of 2		XP_011516104.2	P30837A0A384MTJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1B1	ENST00000377698.4 link	c.183C>T	p.Thr61Thr	synonymous_variant	Exon 2 of 2	1	NM_000692.5	ENSP00000366927.3		P30837
ALDH1B1	ENST00000635162.1 link	c.183C>T	p.Thr61Thr	synonymous_variant	Exon 3 of 3	3		ENSP00000489053.1		A0A0U1RQK9

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27559

AN:

152096

Hom.:

2865

Cov.:

show subpopulations

Gnomad AFR

AF:

0.223

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.174

GnomAD3 exomes

AF:

0.198

AC:

49618

AN:

250902

Hom.:

5995

AF XY:

0.192

AC XY:

26061

AN XY:

135674

show subpopulations

Gnomad AFR exome

AF:

0.229

Gnomad AMR exome

AF:

0.330

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.377

Gnomad SAS exome

AF:

0.251

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.150

AC:

219451

AN:

1461480

Hom.:

19177

Cov.:

AF XY:

0.152

AC XY:

110671

AN XY:

727068

show subpopulations

Gnomad4 AFR exome

AF:

0.224

Gnomad4 AMR exome

AF:

0.319

Gnomad4 ASJ exome

AF:

0.133

Gnomad4 EAS exome

AF:

0.361

Gnomad4 SAS exome

AF:

0.254

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.181

AC:

27596

AN:

152214

Hom.:

2874

Cov.:

AF XY:

0.186

AC XY:

13816

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.223

Gnomad4 AMR

AF:

0.246

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.382

Gnomad4 SAS

AF:

0.270

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.126

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.136

Hom.:

3175

Bravo

AF:

0.189

Asia WGS

AF:

0.307

AC:

1064

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Aug 29, 2013

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.034

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over