rs2511989

chr11-57610852-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000062.3(SERPING1):c.1030-865C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,014 control chromosomes in the GnomAD database, including 11,774 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.39 (11774 hom., cov: 32)
• Consequence: SERPING1 NM_000062.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.452

Genes affected

SERPING1 (HGNC:1228): (serpin family G member 1) This gene encodes a highly glycosylated plasma protein involved in the regulation of the complement cascade. Its encoded protein, C1 inhibitor, inhibits activated C1r and C1s of the first complement component and thus regulates complement activation. It is synthesized in the liver, and its deficiency is associated with hereditary angioneurotic oedema (HANE). Alternative splicing results in multiple transcript variants encoding the same isoform. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 11-57610852-C-T is Benign according to our data. Variant chr11-57610852-C-T is described in ClinVar as [Benign]. Clinvar id is 983234.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-57610852-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERPING1	NM_000062.3	c.1030-865C>T		intron_variant		ENST00000278407.9
SERPING1	NM_001032295.2	c.1030-865C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERPING1	ENST00000278407.9	c.1030-865C>T		intron_variant		1	NM_000062.3	P2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58952 AN: 151896 Hom.: 11762 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.388 AC: 59005 AN: 152014 Hom.: 11774 Cov.: 32 AF XY: 0.382 AC XY: 28374 AN XY: 74298

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.374

Alfa AF: 0.398 Hom.: 6852

Bravo AF: 0.385

Asia WGS AF: 0.260 AC: 908 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary angioedema type 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

CeMIA

-

This variant is considered likely benign or benign based on one or more of the following criteria: allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (BA1), allele frequency is greater than expected for disorder (BS1), it is observed in a healthy adult individual (BS2), it is predicted to be benign by multiple in silico algorithms (BP4), it is found in a case with an alternate molecular basis for the disease (BP5) and/or reputable source recently reports variant as benign (BP6). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.60
Dann	Benign	0.64

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: rs2511989; hg19: chr11-57378325;