chr13-114179053-T-C

Variant names:

• chr13-114179053-T-C
• rs9525291
• ENST00000643687.1:c.-268-10T>C

Variant summary

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

Genes affected

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

ENSG00000283347 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP97D2	NM_001395229.1	c.-278T>C		upstream_gene_variant		ENST00000636692.2	NP_001382158.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP97D2	ENST00000636692.2	c.-278T>C		upstream_gene_variant		5	NM_001395229.1	ENSP00000489989.1

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

African (AFR) AF: 0.241 AC: 932 AN: 3864

American (AMR) AF: 0.267 AC: 855 AN: 3202

Ashkenazi Jewish (ASJ) AF: 0.0172 AC: 82 AN: 4778

East Asian (EAS) AF: 0.509 AC: 4886 AN: 9592

South Asian (SAS) AF: 0.221 AC: 216 AN: 978

European-Finnish (FIN) AF: 0.0862 AC: 637 AN: 7394

Middle Eastern (MID) AF: 0.0731 AC: 45 AN: 616

European-Non Finnish (NFE) AF: 0.0669 AC: 5066 AN: 75672

Other (OTH) AF: 0.108 AC: 852 AN: 7918

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

African (AFR) AF: 0.255 AC: 10495 AN: 41172

American (AMR) AF: 0.235 AC: 3580 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3466

East Asian (EAS) AF: 0.460 AC: 2354 AN: 5122

South Asian (SAS) AF: 0.240 AC: 1146 AN: 4778

European-Finnish (FIN) AF: 0.0858 AC: 898 AN: 10468

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0748 AC: 5076 AN: 67836

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.108 Hom.: 1846

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
PhyloP100		-0.66
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9525291; hg19: chr13-114944528;