rs7617733

Positions:

• chr3-126171901-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012190.4(ALDH1L1):​c.-24+8575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,966 control chromosomes in the GnomAD database, including 4,756 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 (4756 hom., cov: 32)
• Consequence: ALDH1L1 NM_012190.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

ALDH1L1 (HGNC:3978): (aldehyde dehydrogenase 1 family member L1) The protein encoded by this gene catalyzes the conversion of 10-formyltetrahydrofolate, nicotinamide adenine dinucleotide phosphate (NADP+), and water to tetrahydrofolate, NADPH, and carbon dioxide. The encoded protein belongs to the aldehyde dehydrogenase family. Loss of function or expression of this gene is associated with decreased apoptosis, increased cell motility, and cancer progression. There is an antisense transcript that overlaps on the opposite strand with this gene locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH1L1	NM_012190.4	c.-24+8575C>T		intron_variant		ENST00000393434.7	NP_036322.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH1L1	ENST00000393434.7	c.-24+8575C>T		intron_variant		1	NM_012190.4	ENSP00000377083.3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35670 AN: 151848 Hom.: 4738 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.235 AC: 35740 AN: 151966 Hom.: 4756 Cov.: 32 AF XY: 0.235 AC XY: 17465 AN XY: 74262

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.216

Alfa AF: 0.180 Hom.: 3532

Bravo AF: 0.245

Asia WGS AF: 0.212 AC: 735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.46

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

Other links and lift over

dbSNP: rs7617733; hg19: chr3-125890744;