13-114173921-A-G

Position:

• chr13-114173921-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP97D2	ENST00000643687.1	c.-1153-2439A>G		intron_variant				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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.0943

Gnomad4 NFE AF: 0.0871

Gnomad4 OTH AF: 0.137

Alfa AF: 0.0994 Hom.: 1907

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11147317; hg19: chr13-114939396;