rs10519307

Variant names:

• chr15-81009925-G-A
• rs10519307
• ENST00000560091.5:c.-142+2794G>A

Variant summary

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

The ENST00000560091.5(CFAP161):​c.-142+2794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,124 control chromosomes in the GnomAD database, including 1,599 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 (1599 hom., cov: 32)
• Consequence: CFAP161 ENST00000560091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

Genes affected

CFAP161 (HGNC:26782): (cilia and flagella associated protein 161)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 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
CFAP161	ENST00000560091.5	c.-142+2794G>A		intron_variant	Intron 1 of 4	5		ENSP00000453414.1

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22014 AN: 152006 Hom.: 1591 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.145 AC: 22029 AN: 152124 Hom.: 1599 Cov.: 32 AF XY: 0.142 AC XY: 10546 AN XY: 74366

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.165

Alfa AF: 0.138 Hom.: 196

Bravo AF: 0.153

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519307; hg19: chr15-81302266;