rs1439911743

Variant names:

• chr9-130499504-GCATGAA-G
• rs1439911743
• NM_054012.4:c.1129_1134delATGAAC

Your query was ambiguous. Multiple possible variants found:

• chr9-130499504-GCATGAAC-GC
• chr9-130499504-GCATGAAC-GG

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PM4

The NM_054012.4(ASS1):​c.1129_1134delATGAAC​(p.Met377_Asn378del) variant causes a conservative 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 conservative_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 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 rank	MANE	Protein	UniProt
ASS1	NM_054012.4	c.1129_1134delATGAAC	p.Met377_Asn378del	conservative_inframe_deletion, splice_region_variant	Exon 14 of 15	ENST00000352480.10	NP_446464.1
ASS1	NM_000050.4	c.1129_1134delATGAAC	p.Met377_Asn378del	conservative_inframe_deletion, splice_region_variant	Exon 15 of 16		NP_000041.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASS1	ENST00000352480.10	c.1129_1134delATGAAC	p.Met377_Asn378del	conservative_inframe_deletion, splice_region_variant	Exon 14 of 15	1	NM_054012.4	ENSP00000253004.6
ASS1	ENST00000372393.7	c.1129_1134delATGAAC	p.Met377_Asn378del	conservative_inframe_deletion, splice_region_variant	Exon 15 of 16	5		ENSP00000361469.2
ASS1	ENST00000372394.5	c.1129_1134delATGAAC	p.Met377_Asn378del	conservative_inframe_deletion, splice_region_variant	Exon 15 of 16	2		ENSP00000361471.1
ASS1	ENST00000372386.6	n.400_405delATGAAC		splice_region_variant, non_coding_transcript_exon_variant	Exon 5 of 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;