rs389862

Variant names:

• chr13-114164754-C-A
• rs389862
• ENST00000643687.1:c.-1154+9970C>A

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP97D2	ENST00000643687.1	c.-1154+9970C>A		intron_variant	Intron 1 of 4			ENSP00000496288.1

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;