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. The variant received -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
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643687.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D2	ENST00000643687.1		c.-1154+9970C>A		intron	N/A	ENSP00000496288.1	A0A2R8Y7P9

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

African (AFR) AF: 0.220 AC: 9131 AN: 41472

American (AMR) AF: 0.145 AC: 2221 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2017 AN: 5142

South Asian (SAS) AF: 0.236 AC: 1133 AN: 4806

European-Finnish (FIN) AF: 0.0844 AC: 895 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5121 AN: 67998

Other (OTH) AF: 0.130 AC: 274 AN: 2108

Alfa AF: 0.0978 Hom.: 4122

Bravo AF: 0.144

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.82
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs389862;

hg19: chr13-114930229;