rs7070

Positions:

• chr14-94593044-A-G
• chr14-94593044-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

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]

LOC112268127 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SERPINA5	NM_000624.6	c.*805A>G		3_prime_UTR_variant	6/6	ENST00000329597.12
LOC112268127	XR_002957587.2	n.2738T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPINA5	ENST00000329597.12	c.*805A>G		3_prime_UTR_variant	6/6	1	NM_000624.6	P1
SERPINA5	ENST00000554276.1	c.*805A>G		3_prime_UTR_variant	5/5	1		P1
SERPINA5	ENST00000554866.5	c.*805A>G		3_prime_UTR_variant	5/5	5		P1

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60133 AN: 151822 Hom.: 12946 Cov.: 32

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: 3 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.396 AC: 60142 AN: 151942 Hom.: 12946 Cov.: 32 AF XY: 0.394 AC XY: 29293 AN XY: 74264

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.0866

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.401

Alfa AF: 0.462 Hom.: 15200

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
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7070; hg19: chr14-95059381;