3-167445582-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006217.6(SERPINI2):c.1141+810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,092 control chromosomes in the GnomAD database, including 4,123 homozygotes. 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: 𝑓 0.19 (4123 hom., cov: 33)
• Consequence: SERPINI2 NM_006217.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINI2	NM_006217.6	c.1141+810G>A		intron_variant		ENST00000264677.9
SERPINI2	NM_001012303.3	c.1141+810G>A		intron_variant
SERPINI2	NM_001394327.1	c.1141+810G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINI2	ENST00000264677.9	c.1141+810G>A		intron_variant		1	NM_006217.6	P1
SERPINI2	ENST00000461846.5	c.1141+810G>A		intron_variant		1		P1
SERPINI2	ENST00000471111.5	c.1141+810G>A		intron_variant		1		P1
SERPINI2	ENST00000495108.1	n.614+810G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28999 AN: 151974 Hom.: 4108 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.191 AC: 29063 AN: 152092 Hom.: 4123 Cov.: 33 AF XY: 0.189 AC XY: 14037 AN XY: 74360

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.0933

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.160

Alfa AF: 0.144 Hom.: 309

Bravo AF: 0.211

Asia WGS AF: 0.209 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.23
Dann	Benign	0.23

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

Publications

LitVar

Other links and lift over

dbSNP: rs7635553; hg19: chr3-167163370;