11-102047491-G-C

Variant names:

• chr11-102047491-G-C
• rs1206991035
• NM_032930.3:c.21G>C

Variant summary

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

The NM_032930.3(CFAP300):​c.21G>C​(p.Gly7Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000723 in 1,383,648 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: CFAP300 NM_032930.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

Genes affected

CFAP300 (HGNC:28188): (cilia and flagella associated protein 300) Predicted to be located in cytoplasm and motile cilium. Implicated in primary ciliary dyskinesia 38. [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=-0.83).
• BP7: Synonymous conserved (PhyloP=0.041 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP300	NM_032930.3	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 7	ENST00000434758.7	NP_116319.2
CFAP300	NM_001363505.2	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 6		NP_001350434.1
CFAP300	NM_001195005.2	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 4		NP_001181934.1
CFAP300	XM_005271713.5	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 6		XP_005271770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP300	ENST00000434758.7	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 7	2	NM_032930.3	ENSP00000414390.2
CFAP300	ENST00000534360.1	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 4	1		ENSP00000435482.1
CFAP300	ENST00000530659.1	n.24G>C		non_coding_transcript_exon_variant	Exon 1 of 6	1
CFAP300	ENST00000526781.5	c.21G>C	p.Gly7Gly	synonymous_variant	Exon 1 of 6	3		ENSP00000433074.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000730 AC: 1 AN: 136904 Hom.: 0 AF XY: 0.0000134 AC XY: 1 AN XY: 74350

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000409

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.23e-7 AC: 1 AN: 1383648 Hom.: 0 Cov.: 31 AF XY: 0.00000146 AC XY: 1 AN XY: 682788

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000280

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs1206991035; hg19: chr11-101918222;