rs12992408

chr2-55521949-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080667.7(CFAP36):c.116-153T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,008 control chromosomes in the GnomAD database, including 3,900 homozygotes. 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: 𝑓 0.22 (3900 hom., cov: 32)
• Consequence: CFAP36 NM_080667.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

Genes affected

CFAP36 (HGNC:30540): (cilia and flagella associated protein 36) Enables protein N-terminus binding activity. Located in ciliary transition zone. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP36	NM_080667.7	c.116-153T>G		intron_variant		ENST00000349456.9
CFAP36	NM_001282761.2	c.191-153T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP36	ENST00000349456.9	c.116-153T>G		intron_variant		1	NM_080667.7	P1

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33827 AN: 151890 Hom.: 3891 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.223 AC: 33856 AN: 152008 Hom.: 3900 Cov.: 32 AF XY: 0.224 AC XY: 16635 AN XY: 74328

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.227

Alfa AF: 0.202 Hom.: 5166

Bravo AF: 0.229

Asia WGS AF: 0.268 AC: 931 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.7
Dann	Benign	0.68

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: rs12992408; hg19: chr2-55749085;