11-68027885-G-C

Variant names:

• chr11-68027885-G-C
• rs3751082
• NM_000694.4:c.1353G>C

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_000694.4(ALDH3B1):​c.1353G>C​(p.Leu451Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ALDH3B1 NM_000694.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 20 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP7: Synonymous conserved (PhyloP=0.624 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000694.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH3B1	NM_000694.4	MANE Select	c.1353G>C	p.Leu451Leu	synonymous	Exon 10 of 10	NP_000685.1
	ALDH3B1	NM_001161473.3		c.1353G>C	p.Leu451Leu	synonymous	Exon 10 of 10	NP_001154945.1
	ALDH3B1	NM_001030010.3		c.1242G>C	p.Leu414Leu	synonymous	Exon 9 of 9	NP_001025181.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH3B1	ENST00000342456.11	TSL:1 MANE Select	c.1353G>C	p.Leu451Leu	synonymous	Exon 10 of 10	ENSP00000473990.2
	ALDH3B1	ENST00000614849.4	TSL:1	c.1353G>C	p.Leu451Leu	synonymous	Exon 10 of 10	ENSP00000478486.1
	ALDH3B1	ENST00000617288.4	TSL:1	c.1242G>C	p.Leu414Leu	synonymous	Exon 9 of 9	ENSP00000481604.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.78
PhyloP100		0.62

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: rs3751082; hg19: chr11-67795353;