rs8177800

chr9-113391819-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000031.6(ALAD):c.165-196G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.055 in 152,246 control chromosomes in the GnomAD database, including 284 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.055 (284 hom., cov: 32)
• Consequence: ALAD NM_000031.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.834

Genes affected

ALAD (HGNC:395): (aminolevulinate dehydratase) The ALAD enzyme is composed of 8 identical subunits and catalyzes the condensation of 2 molecules of delta-aminolevulinate to form porphobilinogen (a precursor of heme, cytochromes and other hemoproteins). ALAD catalyzes the second step in the porphyrin and heme biosynthetic pathway; zinc is essential for enzymatic activity. ALAD enzymatic activity is inhibited by lead and a defect in the ALAD structural gene can cause increased sensitivity to lead poisoning and acute hepatic porphyria. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 9-113391819-C-T is Benign according to our data. Variant chr9-113391819-C-T is described in ClinVar as [Benign]. Clinvar id is 1242974.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALAD	NM_000031.6	c.165-196G>A		intron_variant		ENST00000409155.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALAD	ENST00000409155.8	c.165-196G>A		intron_variant		1	NM_000031.6	P1

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8368 AN: 152128 Hom.: 283 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0533

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0790

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0550 AC: 8375 AN: 152246 Hom.: 284 Cov.: 32 AF XY: 0.0541 AC XY: 4030 AN XY: 74456

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0533

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.0790

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0677 Hom.: 102

Bravo AF: 0.0529

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.7
Dann	Benign	0.53

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: rs8177800; hg19: chr9-116154099;