rs2048271

Positions:

• chr15-81134966-G-A

Variant summary

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

The NM_173528.4(CFAP161):​c.70-304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,072 control chromosomes in the GnomAD database, including 23,794 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 0.53 (23794 hom., cov: 32)
• Consequence: CFAP161 NM_173528.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP161	NM_173528.4	c.70-304G>A		intron_variant		ENST00000286732.5	NP_775799.2
CFAP161	NM_001353365.2	c.70-304G>A		intron_variant			NP_001340294.1
CFAP161	XM_006720408.3	c.-6-304G>A		intron_variant			XP_006720471.1
CFAP161	XM_017021963.2	c.-6-304G>A		intron_variant			XP_016877452.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000286732.5	c.70-304G>A		intron_variant		1	NM_173528.4	ENSP00000286732.4
CFAP161	ENST00000560091.5	c.-6-304G>A		intron_variant		5		ENSP00000453414.1
CFAP161	ENST00000561216.1	c.-6-304G>A		intron_variant		4		ENSP00000454135.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80366 AN: 151956 Hom.: 23796 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.529 AC: 80384 AN: 152072 Hom.: 23794 Cov.: 32 AF XY: 0.523 AC XY: 38865 AN XY: 74332

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.553

Alfa AF: 0.624 Hom.: 15088

Bravo AF: 0.509

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.035
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048271; hg19: chr15-81427307; COSMIC: COSV54429030;