chr11-57607398-C-G

Variant names:

• chr11-57607398-C-G
• rs11229066
• NM_000062.3:c.1029+851C>G

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.1029+851C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,064 control chromosomes in the GnomAD database, including 3,912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.21 (3912 hom., cov: 32)
• Consequence: SERPING1 NM_000062.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.17

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=-0.92).
• BP6: Variant 11-57607398-C-G is Benign according to our data. Variant chr11-57607398-C-G is described in ClinVar as [Benign]. Clinvar id is 983255.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-57607398-C-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SERPING1	NM_000062.3	c.1029+851C>G		intron_variant	Intron 6 of 7	ENST00000278407.9	NP_000053.2
SERPING1	NM_001032295.2	c.1029+851C>G		intron_variant	Intron 5 of 6		NP_001027466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SERPING1	ENST00000278407.9	c.1029+851C>G		intron_variant	Intron 6 of 7	1	NM_000062.3	ENSP00000278407.4

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32216 AN: 151946 Hom.: 3912 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.212 AC: 32216 AN: 152064 Hom.: 3912 Cov.: 32 AF XY: 0.213 AC XY: 15811 AN XY: 74330

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.233

Alfa AF: 0.146 Hom.: 318

Bravo AF: 0.196

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary angioedema type 1 Benign:1

-

CeMIA

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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	-0.92
CADD	Benign	0.48
DANN	Benign	0.23

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: rs11229066; hg19: chr11-57374871;