rs2683238

Positions:

• chr15-81113282-G-A
• chr15-81113282-G-C

Variant summary

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

The ENST00000561216.1(CFAP161):​c.-142+13761G>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 ENST00000561216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP161	XM_006720408.3	c.-142+13761G>A		intron_variant			XP_006720471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000560091.5	c.-141-14308G>A		intron_variant		5		ENSP00000453414.1
CFAP161	ENST00000561216.1	c.-142+13761G>A		intron_variant		4		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

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.558

Alfa AF: 0.627 Hom.: 12702

Bravo AF: 0.531

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2683238; hg19: chr15-81405623;