13-114158302-G-C

Variant summary

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

The ENST00000643687.1(CFAP97D2):c.-1154+3518G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,900 control chromosomes in the GnomAD database, including 16,072 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 0.45 (16072 hom., cov: 32)
• Consequence: CFAP97D2 ENST00000643687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

CFAP97D2 (HGNC:53789): (CFAP97 domain containing 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP97D2	ENST00000643687.1	c.-1154+3518G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68742 AN: 151782 Hom.: 16055 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.453 AC: 68802 AN: 151900 Hom.: 16072 Cov.: 32 AF XY: 0.455 AC XY: 33735 AN XY: 74224

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.440

Alfa AF: 0.237 Hom.: 468

Bravo AF: 0.468

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.42
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9562080; hg19: chr13-114923777;