chr3-52213094-G-A

Position:

• chr3-52213094-G-A

Variant summary

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

The NM_000688.6(ALAS1):​c.1762+674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,900 control chromosomes in the GnomAD database, including 17,782 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 0.48 (17782 hom., cov: 31)
• Consequence: ALAS1 NM_000688.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

ALAS1 (HGNC:396): (5'-aminolevulinate synthase 1) This gene encodes the mitochondrial enzyme which is catalyzes the rate-limiting step in heme (iron-protoporphyrin) biosynthesis. The enzyme encoded by this gene is the housekeeping enzyme; a separate gene encodes a form of the enzyme that is specific for erythroid tissue. The level of the mature encoded protein is regulated by heme: high levels of heme down-regulate the mature enzyme in mitochondria while low heme levels up-regulate. A pseudogene of this gene is located on chromosome 12. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALAS1	NM_000688.6	c.1762+674G>A		intron_variant		ENST00000484952.6	NP_000679.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALAS1	ENST00000484952.6	c.1762+674G>A		intron_variant		1	NM_000688.6	ENSP00000418779.1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72245 AN: 151782 Hom.: 17772 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.476 AC: 72286 AN: 151900 Hom.: 17782 Cov.: 31 AF XY: 0.472 AC XY: 35051 AN XY: 74222

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.494

Alfa AF: 0.516 Hom.: 25937

Bravo AF: 0.474

Asia WGS AF: 0.414 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.95
DANN	Benign	0.69

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: rs352163; hg19: chr3-52247110;