rs10484047

Variant names:

• chr14-94582891-G-A
• rs10484047
• NM_000624.6:c.-18+1181G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-94582891-G-A
• chr14-94582891-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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]

ENSG00000294537 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000624.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINA5	NM_000624.6	MANE Select	c.-18+1181G>A		intron	N/A	NP_000615.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SERPINA5	ENST00000329597.12	TSL:1 MANE Select	c.-18+1181G>A		intron	N/A	ENSP00000333203.7
	SERPINA5	ENST00000554276.1	TSL:1	c.-18+1181G>A		intron	N/A	ENSP00000451610.1
	ENSG00000294537	ENST00000724260.1		n.833C>T		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.268 AC: 11116 AN: 41480

American (AMR) AF: 0.188 AC: 2874 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3470

East Asian (EAS) AF: 0.161 AC: 831 AN: 5176

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4818

European-Finnish (FIN) AF: 0.134 AC: 1422 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8995 AN: 67998

Other (OTH) AF: 0.172 AC: 364 AN: 2116

Alfa AF: 0.147 Hom.: 2286

Bravo AF: 0.185

Asia WGS AF: 0.167 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

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: rs10484047; hg19: chr14-95049228;