rs1509545

Variant names:

• chr15-81127591-T-A
• rs1509545
• ENST00000560091.5:c.-140T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000560091.5(CFAP161):​c.-140T>A variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: CFAP161 ENST00000560091.5 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 0 publications found

Genes affected

CFAP161 (HGNC:26782): (cilia and flagella associated protein 161)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP161	XM_006720408.3	c.-140T>A		splice_region_variant	Exon 2 of 8		XP_006720471.1
CFAP161	XM_017021963.2	c.-140T>A		splice_region_variant	Exon 2 of 8		XP_016877452.1
CFAP161	XM_006720408.3	c.-140T>A		5_prime_UTR_variant	Exon 2 of 8		XP_006720471.1
CFAP161	XM_017021963.2	c.-140T>A		5_prime_UTR_variant	Exon 2 of 8		XP_016877452.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP161	ENST00000560091.5	c.-140T>A		splice_region_variant	Exon 2 of 5	5		ENSP00000453414.1
CFAP161	ENST00000561216.1	c.-140T>A		splice_region_variant	Exon 2 of 4	4		ENSP00000454135.1
CFAP161	ENST00000560091.5	c.-140T>A		5_prime_UTR_variant	Exon 2 of 5	5		ENSP00000453414.1
CFAP161	ENST00000561216.1	c.-140T>A		5_prime_UTR_variant	Exon 2 of 4	4		ENSP00000454135.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.30
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1509545; hg19: chr15-81419932;