rs376183132

Variant names:

• chr12-7062107-TAAAAA-T
• rs376183132
• NM_001734.5:c.5+200_5+204delAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr12-7062107-TAAAAA-T
• chr12-7062107-TAAAAA-TA
• chr12-7062107-TAAAAA-TAA
• chr12-7062107-TAAAAA-TAAA
• chr12-7062107-TAAAAA-TAAAA
• chr12-7062107-TAAAAA-TAAAAAA
• chr12-7062107-TAAAAA-TAAAAAAA
• chr12-7062107-TAAAAA-TAAAAAAAA
• chr12-7062107-TAAAAA-TAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001734.5(C1S):​c.5+200_5+204delAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000705 in 141,944 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000070 (0 hom., cov: 27)
• Consequence: C1S NM_001734.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

C1S (HGNC:1247): (complement C1s) This gene encodes a serine protease, which is a major constituent of the human complement subcomponent C1. C1s associates with two other complement components C1r and C1q in order to yield the first component of the serum complement system. Defects in this gene are the cause of selective C1s deficiency. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1S	NM_001734.5	c.5+200_5+204delAAAAA		intron_variant	Intron 2 of 11	ENST00000360817.10	NP_001725.1
C1S	NM_201442.4	c.5+200_5+204delAAAAA		intron_variant	Intron 2 of 11		NP_958850.1
C1S	NM_001346850.2	c.-289+200_-289+204delAAAAA		intron_variant	Intron 2 of 10		NP_001333779.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1S	ENST00000360817.10	c.5+200_5+204delAAAAA		intron_variant	Intron 2 of 11	1	NM_001734.5	ENSP00000354057.5

Frequencies

GnomAD3 genomes AF: 0.00000705 AC: 1 AN: 141944 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.0000260

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000705 AC: 1 AN: 141944 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 68794

Gnomad4 AFR AF: 0.0000260

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs376183132; hg19: chr12-7169411;