11-101915297-A-C

Variant names:

• chr11-101915297-A-C
• rs145606538
• NM_020802.4:c.13A>C

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_020802.4(CEP126):​c.13A>C​(p.Arg5Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CEP126 NM_020802.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

CEP126 (HGNC:29264): (centrosomal protein 126) Involved in cilium assembly; cytoplasmic microtubule organization; and mitotic spindle organization. Located in centrosome; ciliary base; and midbody. [provided by Alliance of Genome Resources, Apr 2022]

ANGPTL5 (HGNC:19705): (angiopoietin like 5) Predicted to be active in collagen-containing extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BP7: Synonymous conserved (PhyloP=1.6 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP126	NM_020802.4	c.13A>C	p.Arg5Arg	synonymous_variant	Exon 1 of 11	ENST00000263468.13	NP_065853.3
ANGPTL5	NM_178127.5	c.-93+722T>G		intron_variant	Intron 1 of 8	ENST00000334289.7	NP_835228.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP126	ENST00000263468.13	c.13A>C	p.Arg5Arg	synonymous_variant	Exon 1 of 11	1	NM_020802.4	ENSP00000263468.8
ANGPTL5	ENST00000334289.7	c.-93+722T>G		intron_variant	Intron 1 of 8	1	NM_178127.5	ENSP00000335255.3
CEP126	ENST00000670091.1	n.13A>C		non_coding_transcript_exon_variant	Exon 1 of 12			ENSP00000499679.1
CEP126	ENST00000670318.1	n.13A>C		non_coding_transcript_exon_variant	Exon 1 of 12			ENSP00000499404.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	13
DANN	Benign	0.75

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: rs145606538; hg19: chr11-101786028;