rs389862

Positions:

• chr13-114164754-C-A
• chr13-114164754-C-T

Variant summary

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

The ENST00000643687.1(CFAP97D2):​c.-1154+9970C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,090 control chromosomes in the GnomAD database, including 1,988 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 0.14 (1988 hom., cov: 31)
• Consequence: CFAP97D2 ENST00000643687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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+9970C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20930 AN: 151972 Hom.: 1987 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.138 AC: 20950 AN: 152090 Hom.: 1988 Cov.: 31 AF XY: 0.142 AC XY: 10541 AN XY: 74350

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.0844

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.130

Alfa AF: 0.0844 Hom.: 1342

Bravo AF: 0.144

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs389862; hg19: chr13-114930229;