ENST00000560091.5:c.-141-20204G>A

Variant names:

• chr15-81107386-G-A
• rs2663944
• ENST00000560091.5:c.-141-20204G>A

Variant summary

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

The ENST00000560091.5(CFAP161):​c.-141-20204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,112 control chromosomes in the GnomAD database, including 29,645 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 0.62 (29645 hom., cov: 32)
• Consequence: CFAP161 ENST00000560091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560091.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP161	ENST00000560091.5	TSL:5	c.-141-20204G>A		intron	N/A	ENSP00000453414.1
	CFAP161	ENST00000561216.1	TSL:4	c.-142+7865G>A		intron	N/A	ENSP00000454135.1

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93930 AN: 151994 Hom.: 29627 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.618 AC: 93985 AN: 152112 Hom.: 29645 Cov.: 32 AF XY: 0.608 AC XY: 45188 AN XY: 74342

African (AFR) AF: 0.636 AC: 26375 AN: 41490

American (AMR) AF: 0.480 AC: 7333 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2416 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1581 AN: 5174

South Asian (SAS) AF: 0.521 AC: 2511 AN: 4816

European-Finnish (FIN) AF: 0.574 AC: 6069 AN: 10564

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45657 AN: 68006

Other (OTH) AF: 0.622 AC: 1314 AN: 2114

Alfa AF: 0.648 Hom.: 38879

Bravo AF: 0.609

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.39
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2663944; hg19: chr15-81399727;