ENST00000560091.5:c.-141-14308G>A

Variant names:

• chr15-81113282-G-A
• rs2683238
• ENST00000560091.5:c.-141-14308G>A

Variant summary

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

The ENST00000560091.5(CFAP161):​c.-141-14308G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,990 control chromosomes in the GnomAD database, including 24,101 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 0.55 (24101 hom., cov: 31)
• Consequence: CFAP161 ENST00000560091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP161	ENST00000560091.5	TSL:5	c.-141-14308G>A		intron	N/A	ENSP00000453414.1
	CFAP161	ENST00000561216.1	TSL:4	c.-142+13761G>A		intron	N/A	ENSP00000454135.1

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83313 AN: 151872 Hom.: 24090 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.548 AC: 83350 AN: 151990 Hom.: 24101 Cov.: 31 AF XY: 0.539 AC XY: 40070 AN XY: 74278

African (AFR) AF: 0.421 AC: 17456 AN: 41424

American (AMR) AF: 0.450 AC: 6876 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2417 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5164

South Asian (SAS) AF: 0.439 AC: 2111 AN: 4812

European-Finnish (FIN) AF: 0.571 AC: 6024 AN: 10548

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45229 AN: 67968

Other (OTH) AF: 0.558 AC: 1176 AN: 2108

Alfa AF: 0.627 Hom.: 14428

Bravo AF: 0.531

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2683238; hg19: chr15-81405623;