NM_006217.6:c.*63G>T

Variant names:

• chr3-167442046-C-A
• rs9844202
• NM_006217.6:c.*63G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006217.6(SERPINI2):​c.*63G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000891 in 1,122,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 8.9e-7 (0 hom.)
• Consequence: SERPINI2 NM_006217.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 13 publications found

Genes affected

SERPINI2 (HGNC:8945): (serpin family I member 2) The gene encodes a member of a family of proteins that acts as inhibitors of serine proteases. These proteins function in the regulation of a variety of physiological processes, including coagulation, fibrinolysis, development, malignancy, and inflammation. Expression of the encoded protein may be downregulated during pancreatic carcinogenesis. Alternative splicing results in multiple transcript variants for this gene. [provided by RefSeq, Jan 2013]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINI2	NM_006217.6	c.*63G>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000264677.9	NP_006208.1
SERPINI2	NM_001012303.3	c.*63G>T		3_prime_UTR_variant	Exon 10 of 10		NP_001012303.2
SERPINI2	NM_001394327.1	c.*63G>T		3_prime_UTR_variant	Exon 10 of 10		NP_001381256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINI2	ENST00000264677.9	c.*63G>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_006217.6	ENSP00000264677.4
SERPINI2	ENST00000461846.5	c.*63G>T		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000417692.1
SERPINI2	ENST00000471111.5	c.*63G>T		downstream_gene_variant		1		ENSP00000419407.1
SERPINI2	ENST00000495108.1	n.*21G>T		downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.91e-7 AC: 1 AN: 1122442 Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0 AN XY: 568214

African (AFR) AF: 0.00 AC: 0 AN: 24392

American (AMR) AF: 0.00 AC: 0 AN: 30630

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21774

East Asian (EAS) AF: 0.00 AC: 0 AN: 36186

South Asian (SAS) AF: 0.00 AC: 0 AN: 68612

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47814

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4986

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 839812

Other (OTH) AF: 0.00 AC: 0 AN: 48236

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		0.32

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: rs9844202; hg19: chr3-167159834;