chr11-102047596-A-G

Variant names:

• chr11-102047596-A-G
• rs12804542
• NM_032930.3:c.110+16A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032930.3(CFAP300):​c.110+16A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 1,533,484 control chromosomes in the GnomAD database, including 721,938 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.96 (70793 hom., cov: 33)
  • Exomes 𝑓: 0.97 (651145 hom.)
• Consequence: CFAP300 NM_032930.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.157
• Publications: 9 publications found

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]

CFAP300 Gene-Disease associations (from GenCC):

• ciliary dyskinesia, primary, 38

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae)
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 11-102047596-A-G is Benign according to our data. Variant chr11-102047596-A-G is described in ClinVar as Benign. ClinVar VariationId is 1192590.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032930.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP300	NM_032930.3	MANE Select	c.110+16A>G		intron	N/A	NP_116319.2	Q9BRQ4-1
	CFAP300	NM_001441265.1		c.110+16A>G		intron	N/A	NP_001428194.1
	CFAP300	NM_001363505.2		c.110+16A>G		intron	N/A	NP_001350434.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP300	ENST00000434758.7	TSL:2 MANE Select	c.110+16A>G		intron	N/A	ENSP00000414390.2	Q9BRQ4-1
	CFAP300	ENST00000534360.1	TSL:1	c.110+16A>G		intron	N/A	ENSP00000435482.1	Q9BRQ4-3
	CFAP300	ENST00000530659.1	TSL:1	n.129A>G		non_coding_transcript_exon	Exon 1 of 6

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146722 AN: 152206 Hom.: 70737 Cov.: 33

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.960

GnomAD2 exomes AF: 0.971 AC: 134141 AN: 138130 AF XY: 0.972

Gnomad AFR exome AF: 0.936

Gnomad AMR exome AF: 0.972

Gnomad ASJ exome AF: 0.949

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 0.980

Gnomad NFE exome AF: 0.969

Gnomad OTH exome AF: 0.967

GnomAD4 exome AF: 0.971 AC: 1341102 AN: 1381160 Hom.: 651145 Cov.: 33 AF XY: 0.971 AC XY: 662055 AN XY: 681722

African (AFR) AF: 0.935 AC: 29468 AN: 31524

American (AMR) AF: 0.971 AC: 34633 AN: 35678

Ashkenazi Jewish (ASJ) AF: 0.951 AC: 23921 AN: 25142

East Asian (EAS) AF: 1.00 AC: 35698 AN: 35700

South Asian (SAS) AF: 0.980 AC: 77602 AN: 79162

European-Finnish (FIN) AF: 0.976 AC: 33167 AN: 33984

Middle Eastern (MID) AF: 0.947 AC: 5370 AN: 5668

European-Non Finnish (NFE) AF: 0.971 AC: 1045237 AN: 1076492

Other (OTH) AF: 0.969 AC: 56006 AN: 57810

GnomAD4 genome AF: 0.964 AC: 146836 AN: 152324 Hom.: 70793 Cov.: 33 AF XY: 0.965 AC XY: 71852 AN XY: 74484

African (AFR) AF: 0.939 AC: 39036 AN: 41558

American (AMR) AF: 0.971 AC: 14861 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3328 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5174

South Asian (SAS) AF: 0.981 AC: 4742 AN: 4832

European-Finnish (FIN) AF: 0.978 AC: 10392 AN: 10624

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66129 AN: 68034

Other (OTH) AF: 0.961 AC: 2033 AN: 2116

Alfa AF: 0.967 Hom.: 86439

Bravo AF: 0.961

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not provided (3)
-	-	1	Ciliary dyskinesia, primary, 38 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.73
PhyloP100		-0.16
PromoterAI		0.10	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12804542; hg19: chr11-101918327;