Variant chr7-122079532-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005763.4(AASS):c.2396+65G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 1,358,486 control chromosomes in the GnomAD database, including 214,970 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 32225 hom., cov: 32)

Exomes 𝑓: 0.55 ( 182745 hom. )

Consequence

AASS
NM_005763.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.220

Variant links:

Genes affected

AASS (HGNC:17366): (aminoadipate-semialdehyde synthase) This gene encodes a bifunctional enzyme that catalyzes the first two steps in the mammalian lysine degradation pathway. The N-terminal and the C-terminal portions of this enzyme contain lysine-ketoglutarate reductase and saccharopine dehydrogenase activity, respectively, resulting in the conversion of lysine to alpha-aminoadipic semialdehyde. Mutations in this gene are associated with familial hyperlysinemia. [provided by RefSeq, Jul 2008]

AASS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 7-122079532-C-T is Benign according to our data. Variant chr7-122079532-C-T is described in ClinVar as [Benign]. Clinvar id is 1222873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
AASS	NM_005763.4 linkuse as main transcript	c.2396+65G>A	intron_variant	ENST00000417368.7	NP_005754.2
AASS	XM_011515725.3 linkuse as main transcript	c.2300+65G>A	intron_variant		XP_011514027.1
AASS	XM_047419710.1 linkuse as main transcript	c.2396+65G>A	intron_variant		XP_047275666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AASS	ENST00000417368.7 linkuse as main transcript	c.2396+65G>A		intron_variant		1	NM_005763.4	ENSP00000403768	P1

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95852

AN:

151922

Hom.:

32147

Cov.:

show subpopulations

Gnomad AFR

AF:

0.886

Gnomad AMI

AF:

0.437

Gnomad AMR

AF:

0.541

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.585

Gnomad FIN

AF:

0.475

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.535

Gnomad OTH

AF:

0.585

GnomAD4 exome

AF:

0.547

AC:

659917

AN:

1206446

Hom.:

182745

Cov.:

AF XY:

0.546

AC XY:

334698

AN XY:

612532

show subpopulations

Gnomad4 AFR exome

AF:

0.905

Gnomad4 AMR exome

AF:

0.513

Gnomad4 ASJ exome

AF:

0.530

Gnomad4 EAS exome

AF:

0.583

Gnomad4 SAS exome

AF:

0.574

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.536

Gnomad4 OTH exome

AF:

0.555

GnomAD4 genome

AF:

0.631

AC:

95992

AN:

152040

Hom.:

32225

Cov.:

AF XY:

0.626

AC XY:

46520

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.887

Gnomad4 AMR

AF:

0.542

Gnomad4 ASJ

AF:

0.534

Gnomad4 EAS

AF:

0.600

Gnomad4 SAS

AF:

0.584

Gnomad4 FIN

AF:

0.475

Gnomad4 NFE

AF:

0.535

Gnomad4 OTH

AF:

0.589

Alfa

AF:

0.620

Hom.:

4525

Bravo

AF:

0.643

Asia WGS

AF:

0.589

AC:

2049

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 08, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.2

DANN

Benign

0.43

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over