rs105147

Variant names:

• chr11-68025546-T-C
• rs105147
• NM_000694.4:c.1117-463T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000694.4(ALDH3B1):​c.1117-463T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,992 control chromosomes in the GnomAD database, including 20,121 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 0.50 (20121 hom., cov: 31)
• Consequence: ALDH3B1 NM_000694.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 10 publications found

Genes affected

ALDH3B1 (HGNC:410): (aldehyde dehydrogenase 3 family member B1) This gene encodes a member of the aldehyde dehydrogenase protein family. Aldehyde dehydrogenases are a family of isozymes that may play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. The encoded protein is able to oxidize long-chain fatty aldehydes in vitro, and may play a role in protection from oxidative stress. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

GLTC1 (HGNC:56861):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH3B1	NM_000694.4	c.1117-463T>C		intron_variant	Intron 8 of 9	ENST00000342456.11	NP_000685.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH3B1	ENST00000342456.11	c.1117-463T>C		intron_variant	Intron 8 of 9	1	NM_000694.4	ENSP00000473990.2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75937 AN: 151872 Hom.: 20076 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.500 AC: 76040 AN: 151992 Hom.: 20121 Cov.: 31 AF XY: 0.497 AC XY: 36907 AN XY: 74306

African (AFR) AF: 0.690 AC: 28580 AN: 41446

American (AMR) AF: 0.399 AC: 6090 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1337 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2339 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1858 AN: 4816

European-Finnish (FIN) AF: 0.442 AC: 4668 AN: 10570

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29674 AN: 67934

Other (OTH) AF: 0.459 AC: 970 AN: 2114

Alfa AF: 0.449 Hom.: 64501

Bravo AF: 0.504

Asia WGS AF: 0.433 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.6
DANN	Benign	0.90
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs105147; hg19: chr11-67793014;