rs1057519610

Variant names:

• chr14-94379500-GGA-G
• rs1057519610
• NM_000295.5:c.1027_1028delTC

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_000295.5(SERPINA1):​c.1027_1028delTC​(p.Ser343ArgfsTer16) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic,other (no stars). Synonymous variant affecting the same amino acid position (i.e. S343S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 34)
• Consequence: SERPINA1 NM_000295.5 frameshift
• Clinical Significance: Pathogenic; other no assertion criteria provided P:1 O:2
• Conservation: PhyloP100: 5.33
• Publications: 2 publications found

Genes affected

SERPINA1 (HGNC:8941): (serpin family A member 1) The protein encoded by this gene is a serine protease inhibitor belonging to the serpin superfamily whose targets include elastase, plasmin, thrombin, trypsin, chymotrypsin, and plasminogen activator. This protein is produced in the liver, the bone marrow, by lymphocytic and monocytic cells in lymphoid tissue, and by the Paneth cells of the gut. Defects in this gene are associated with chronic obstructive pulmonary disease, emphysema, and chronic liver disease. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2020]

SERPINA1 Gene-Disease associations (from GenCC):

• alpha 1-antitrypsin deficiency

  Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
• hemorrhagic disease due to alpha-1-antitrypsin Pittsburgh mutation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• cystic fibrosis

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 22 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 14-94379500-GGA-G is Pathogenic according to our data. Variant chr14-94379500-GGA-G is described in ClinVar as Pathogenic|other. ClinVar VariationId is 17980.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000295.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINA1	NM_000295.5	MANE Select	c.1027_1028delTC	p.Ser343ArgfsTer16	frameshift	Exon 4 of 5	NP_000286.3
	SERPINA1	NM_001002235.3		c.1027_1028delTC	p.Ser343ArgfsTer16	frameshift	Exon 4 of 5	NP_001002235.1
	SERPINA1	NM_001002236.3		c.1027_1028delTC	p.Ser343ArgfsTer16	frameshift	Exon 6 of 7	NP_001002236.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINA1	ENST00000393087.9	TSL:1 MANE Select	c.1027_1028delTC	p.Ser343ArgfsTer16	frameshift	Exon 4 of 5	ENSP00000376802.4
	SERPINA1	ENST00000355814.8	TSL:1	c.1027_1028delTC	p.Ser343ArgfsTer16	frameshift	Exon 4 of 5	ENSP00000348068.4
	SERPINA1	ENST00000393088.8	TSL:1	c.1027_1028delTC	p.Ser343ArgfsTer16	frameshift	Exon 6 of 7	ENSP00000376803.4

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic; other

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Alpha-1-antitrypsin deficiency (1)
-	-	-	PI NULL(HONG KONG 1) (1)
-	-	-	PI Q0(HONG KONG 1) (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.3
Mutation Taster		=0/200	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs1057519610; hg19: chr14-94845837;