dbSNP rs7070: SERPINA5:c.*805A>G (chr14-94593044-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000624.6(SERPINA5):c.*805A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,948 control chromosomes in the GnomAD database, including 12,946 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 0.40 ( 12946 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

SERPINA5
NM_000624.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21

Publications

6 publications found

Variant links:

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]

SERPINA5 links:

ENSG00000273259 (HGNC:):

ENSG00000273259 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPINA5	NM_000624.6 link	c.*805A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000329597.12	NP_000615.3	P05154A0A024R6N9B4DDH1
LOC112268127	XR_002957587.2 link	n.2738T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPINA5	ENST00000329597.12 link	c.*805A>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_000624.6	ENSP00000333203.7		P05154
ENSG00000273259	ENST00000553947.1 link	n.77+908A>G		intron_variant	Intron 1 of 7	2		ENSP00000452367.2		G3V5I3

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60133

AN:

151822

Hom.:

12946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.536

Gnomad EAS

AF:

0.0866

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.513

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.482

Gnomad OTH

AF:

0.406

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.396

AC:

60142

AN:

151942

Hom.:

12946

Cov.:

AF XY:

0.394

AC XY:

29293

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.287

AC:

11885

AN:

41476

American (AMR)

AF:

0.317

AC:

4798

AN:

15140

Ashkenazi Jewish (ASJ)

AF:

0.536

AC:

1858

AN:

3466

East Asian (EAS)

AF:

0.0866

AC:

449

AN:

5186

South Asian (SAS)

AF:

0.341

AC:

1645

AN:

4826

European-Finnish (FIN)

AF:

0.513

AC:

5425

AN:

10574

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.482

AC:

32788

AN:

67964

Other (OTH)

AF:

0.401

AC:

845

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1793

3585

5378

7170

8963

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.451

Hom.:

18888

Bravo

AF:

0.374

Asia WGS

AF:

0.195

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.058

(source)

DANN

Benign

0.58

PhyloP100

-2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over