rs12593367

Variant names:

• chr15-81042759-G-A
• rs12593367
• ENST00000560091.5:c.-142+35628G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000560091.5	c.-142+35628G>A		intron_variant	Intron 1 of 4	5		ENSP00000453414.1

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

African (AFR) AF: 0.419 AC: 17359 AN: 41442

American (AMR) AF: 0.417 AC: 6354 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3464

East Asian (EAS) AF: 0.541 AC: 2798 AN: 5172

South Asian (SAS) AF: 0.536 AC: 2586 AN: 4822

European-Finnish (FIN) AF: 0.340 AC: 3593 AN: 10558

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21470 AN: 67972

Other (OTH) AF: 0.379 AC: 801 AN: 2114

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
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs12593367; hg19: chr15-81335100;