rs2048271

Variant names:

• chr15-81134966-G-A
• rs2048271
• NM_173528.4:c.70-304G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.93).
• 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 rank	MANE	Protein	UniProt
CFAP161	NM_173528.4	c.70-304G>A		intron_variant	Intron 1 of 6	ENST00000286732.5	NP_775799.2
CFAP161	NM_001353365.2	c.70-304G>A		intron_variant	Intron 1 of 5		NP_001340294.1
CFAP161	XM_006720408.3	c.-6-304G>A		intron_variant	Intron 2 of 7		XP_006720471.1
CFAP161	XM_017021963.2	c.-6-304G>A		intron_variant	Intron 2 of 7		XP_016877452.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000286732.5	c.70-304G>A		intron_variant	Intron 1 of 6	1	NM_173528.4	ENSP00000286732.4
CFAP161	ENST00000560091.5	c.-6-304G>A		intron_variant	Intron 2 of 4	5		ENSP00000453414.1
CFAP161	ENST00000561216.1	c.-6-304G>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.285 AC: 11828 AN: 41486

American (AMR) AF: 0.515 AC: 7871 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2401 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5178

South Asian (SAS) AF: 0.420 AC: 2027 AN: 4822

European-Finnish (FIN) AF: 0.600 AC: 6330 AN: 10546

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46562 AN: 67978

Other (OTH) AF: 0.553 AC: 1169 AN: 2114

Alfa AF: 0.612 Hom.: 21272

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
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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