Variant rs1439911743 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4

The NM_054012.4(ASS1):c.1129_1134del(p.Met377_Asn378del) variant causes a inframe deletion, splice region change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

ASS1
NM_054012.4 inframe_deletion, splice_region

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.20

Variant links:

Genes affected

ASS1 (HGNC:758): (argininosuccinate synthase 1) The protein encoded by this gene catalyzes the penultimate step of the arginine biosynthetic pathway. There are approximately 10 to 14 copies of this gene including the pseudogenes scattered across the human genome, among which the one located on chromosome 9 appears to be the only functional gene for argininosuccinate synthetase. Mutations in the chromosome 9 copy of this gene cause citrullinemia. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2012]

ASS1 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_054012.4.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASS1	NM_054012.4 linkuse as main transcript	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	14/15	ENST00000352480.10	NP_446464.1
ASS1	NM_000050.4 linkuse as main transcript	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	15/16		NP_000041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ASS1	ENST00000352480.10 linkuse as main transcript	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	14/15	1	NM_054012.4	ENSP00000253004	P1
ASS1	ENST00000372393.7 linkuse as main transcript	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	15/16	5		ENSP00000361469	P1
ASS1	ENST00000372394.5 linkuse as main transcript	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	15/16	2		ENSP00000361471	P1
ASS1	ENST00000372386.6 linkuse as main transcript	n.400_405del		splice_region_variant, non_coding_transcript_exon_variant	5/6	3

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.