rs11626091

chr14-94475250-G-A

Variant summary

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

The NM_175739.4(SERPINA9):c.-18+886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,960 control chromosomes in the GnomAD database, including 10,259 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 0.34 (10259 hom., cov: 31)
• Consequence: SERPINA9 NM_175739.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

Genes affected

SERPINA9 (HGNC:15995): (serpin family A member 9) Enables serine-type endopeptidase inhibitor activity. Predicted to be involved in negative regulation of endopeptidase activity. Predicted to be located in cytoplasm and membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINA9	NM_175739.4	c.-18+886C>T		intron_variant		ENST00000674397.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINA9	ENST00000674397.2	c.-18+886C>T		intron_variant			NM_175739.4	P2

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51819 AN: 151842 Hom.: 10257 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.341 AC: 51830 AN: 151960 Hom.: 10259 Cov.: 31 AF XY: 0.341 AC XY: 25340 AN XY: 74290

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.354

Alfa AF: 0.417 Hom.: 17591

Bravo AF: 0.329

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.37
Dann	Benign	0.53

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: rs11626091; hg19: chr14-94941587; COSMIC: COSV54078803;