13-114173921-A-G

Variant names:

• chr13-114173921-A-G
• rs11147317
• ENST00000643687.1:c.-1153-2439A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000643687.1(CFAP97D2):​c.-1153-2439A>G 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 152,218 control chromosomes in the GnomAD database, including 1,838 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 (1838 hom., cov: 33)
• Consequence: CFAP97D2 ENST00000643687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 11 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 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.-1153-2439A>G		intron_variant	Intron 1 of 4			ENSP00000496288.1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21394 AN: 152100 Hom.: 1830 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0871

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.141 AC: 21425 AN: 152218 Hom.: 1838 Cov.: 33 AF XY: 0.141 AC XY: 10492 AN XY: 74412

African (AFR) AF: 0.241 AC: 9987 AN: 41514

American (AMR) AF: 0.166 AC: 2546 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3468

East Asian (EAS) AF: 0.157 AC: 812 AN: 5176

South Asian (SAS) AF: 0.0976 AC: 471 AN: 4824

European-Finnish (FIN) AF: 0.0943 AC: 999 AN: 10592

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0871 AC: 5925 AN: 68024

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.106 Hom.: 4677

Bravo AF: 0.153

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.38
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11147317; hg19: chr13-114939396;