rs1317060

Variant names:

• chr15-81114074-T-C
• rs1317060
• ENST00000560091.5:c.-141-13516T>C

Variant summary

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

The ENST00000560091.5(CFAP161):​c.-141-13516T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,988 control chromosomes in the GnomAD database, including 22,098 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 0.51 (22098 hom., cov: 32)
• Consequence: CFAP161 ENST00000560091.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 5 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=-0.72).
• 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 rank	MANE	Protein	UniProt
CFAP161	XM_006720408.3	c.-141-13516T>C		intron_variant	Intron 1 of 7		XP_006720471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000560091.5	c.-141-13516T>C		intron_variant	Intron 1 of 4	5		ENSP00000453414.1
CFAP161	ENST00000561216.1	c.-141-13516T>C		intron_variant	Intron 1 of 3	4		ENSP00000454135.1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77783 AN: 151870 Hom.: 22093 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.512 AC: 77802 AN: 151988 Hom.: 22098 Cov.: 32 AF XY: 0.505 AC XY: 37496 AN XY: 74288

African (AFR) AF: 0.294 AC: 12163 AN: 41428

American (AMR) AF: 0.440 AC: 6717 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1344 AN: 5172

South Asian (SAS) AF: 0.439 AC: 2113 AN: 4818

European-Finnish (FIN) AF: 0.572 AC: 6036 AN: 10544

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

European-Non Finnish (NFE) AF: 0.665 AC: 45201 AN: 67972

Other (OTH) AF: 0.537 AC: 1135 AN: 2114

Alfa AF: 0.615 Hom.: 133827

Bravo AF: 0.489

Asia WGS AF: 0.312 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.7
DANN	Benign	0.92
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1317060; hg19: chr15-81406415;