ENST00000560091.5:c.-142+59665G>A

Variant names:

• chr15-81066796-G-A
• rs2663905
• ENST00000560091.5:c.-142+59665G>A

Variant summary

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

The ENST00000560091.5(CFAP161):​c.-142+59665G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 151,500 control chromosomes in the GnomAD database, including 44,875 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 0.76 (44875 hom., cov: 32)
• Consequence: CFAP161 ENST00000560091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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+59665G>A		intron_variant	Intron 1 of 4	5		ENSP00000453414.1

Frequencies

GnomAD3 genomes AF: 0.759 AC: 114852 AN: 151380 Hom.: 44827 Cov.: 32

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.759 AC: 114957 AN: 151500 Hom.: 44875 Cov.: 32 AF XY: 0.746 AC XY: 55236 AN XY: 74034

African (AFR) AF: 0.913 AC: 37793 AN: 41398

American (AMR) AF: 0.600 AC: 9129 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2907 AN: 3464

East Asian (EAS) AF: 0.434 AC: 2225 AN: 5132

South Asian (SAS) AF: 0.540 AC: 2594 AN: 4804

European-Finnish (FIN) AF: 0.689 AC: 7149 AN: 10378

Middle Eastern (MID) AF: 0.759 AC: 220 AN: 290

European-Non Finnish (NFE) AF: 0.747 AC: 50635 AN: 67798

Other (OTH) AF: 0.778 AC: 1640 AN: 2108

Alfa AF: 0.757 Hom.: 12641

Bravo AF: 0.758

Asia WGS AF: 0.506 AC: 1735 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2663905; hg19: chr15-81359137;