rs10484047

Positions:

• chr14-94582891-G-A

Variant summary

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

The NM_000624.6(SERPINA5):​c.-18+1181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,162 control chromosomes in the GnomAD database, including 2,614 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 0.18 (2614 hom., cov: 33)
• Consequence: SERPINA5 NM_000624.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

Genes affected

SERPINA5 (HGNC:8723): (serpin family A member 5) The protein encoded by this gene is a member of the serpin family of proteins, a group of proteins that inhibit serine proteases. This gene is one in a cluster of serpin genes located on the q arm of chromosome 14. This family member is a glycoprotein that can inhibit several serine proteases, including protein C and various plasminogen activators and kallikreins, and it thus plays diverse roles in hemostasis and thrombosis in multiple organs. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPINA5	NM_000624.6	c.-18+1181G>A		intron_variant		ENST00000329597.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINA5	ENST00000329597.12	c.-18+1181G>A		intron_variant		1	NM_000624.6	P1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26993 AN: 152046 Hom.: 2606 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.178 AC: 27035 AN: 152162 Hom.: 2614 Cov.: 33 AF XY: 0.177 AC XY: 13153 AN XY: 74388

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.172

Alfa AF: 0.140 Hom.: 1585

Bravo AF: 0.185

Asia WGS AF: 0.167 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.34

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: rs10484047; hg19: chr14-95049228;