rs1439911743

chr9-130499504-GCATGAAC-GCchr9-130499504-GCATGAAC-GG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4

The NM_054012.4(ASS1):c.1129_1134del(p.Met377_Asn378del) variant causes a inframe deletion, splice region change. 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.20

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_054012.4.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASS1	NM_054012.4	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	14/15	ENST00000352480.10
ASS1	NM_000050.4	c.1129_1134del	p.Met377_Asn378del	inframe_deletion, splice_region_variant	15/16

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1439911743; hg19: chr9-133374891;