13-114158302-G-C

Variant names:

• chr13-114158302-G-C
• rs9562080
• ENST00000643687.1:c.-1154+3518G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP97D2	ENST00000643687.1	c.-1154+3518G>C		intron_variant	Intron 1 of 4			ENSP00000496288.1

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

African (AFR) AF: 0.555 AC: 22970 AN: 41388

American (AMR) AF: 0.468 AC: 7142 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1439 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3160 AN: 5172

South Asian (SAS) AF: 0.453 AC: 2186 AN: 4822

European-Finnish (FIN) AF: 0.412 AC: 4348 AN: 10552

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 25995 AN: 67926

Other (OTH) AF: 0.440 AC: 926 AN: 2104

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9562080; hg19: chr13-114923777;