13-114179053-T-C

Position:

• chr13-114179053-T-C

Variant summary

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

The ENST00000643687.1(CFAP97D2):​c.-268-10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 265,382 control chromosomes in the GnomAD database, including 4,680 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 0.16 (2792 hom., cov: 30)
  • Exomes 𝑓: 0.12 (1888 hom.)
• Consequence: CFAP97D2 ENST00000643687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114179053T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP97D2	ENST00000643687.1	c.-268-10T>C		intron_variant				ENSP00000496288.1
ENSG00000283347	ENST00000637433.1	n.415-3408A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23954 AN: 151252 Hom.: 2786 Cov.: 30

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.119 AC: 13571 AN: 114014 Hom.: 1888 Cov.: 0 AF XY: 0.115 AC XY: 6644 AN XY: 57606

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.267

Gnomad4 ASJ exome AF: 0.0172

Gnomad4 EAS exome AF: 0.509

Gnomad4 SAS exome AF: 0.221

Gnomad4 FIN exome AF: 0.0862

Gnomad4 NFE exome AF: 0.0669

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.158 AC: 23978 AN: 151368 Hom.: 2792 Cov.: 30 AF XY: 0.164 AC XY: 12130 AN XY: 73956

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.143

Alfa AF: 0.102 Hom.: 1081

Bravo AF: 0.175

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9525291; hg19: chr13-114944528;