rs12593367

Positions:

• chr15-81042759-G-A
• chr15-81042759-G-C
• chr15-81042759-G-T

Variant summary

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

The ENST00000560091.5(CFAP161):​c.-142+35628G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,000 control chromosomes in the GnomAD database, including 10,891 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 0.37 (10891 hom., cov: 32)
• Consequence: CFAP161 ENST00000560091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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
CFAP161	ENST00000560091.5	c.-142+35628G>A		intron_variant		5		ENSP00000453414

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56191 AN: 151882 Hom.: 10883 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.370 AC: 56227 AN: 152000 Hom.: 10891 Cov.: 32 AF XY: 0.377 AC XY: 27984 AN XY: 74310

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.379

Alfa AF: 0.363 Hom.: 1664

Bravo AF: 0.378

Asia WGS AF: 0.514 AC: 1789 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	0.60
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12593367; hg19: chr15-81335100;