rs2663905

Positions:

• chr15-81066796-G-A
• chr15-81066796-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000560091.5	c.-142+59665G>A		intron_variant		5		ENSP00000453414

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

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.778

Alfa AF: 0.763 Hom.: 5748

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2663905; hg19: chr15-81359137;