rs11000566

Positions:

• chr10-73261924-T-A

Variant summary

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

The NM_001367801.1(CFAP70):​c.3238-5508A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 150,136 control chromosomes in the GnomAD database, including 2,847 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 0.15 (2847 hom., cov: 30)
• Consequence: CFAP70 NM_001367801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

Genes affected

CFAP70 (HGNC:30726): (cilia and flagella associated protein 70) Predicted to be involved in cilium assembly and cilium movement. Located in ciliary basal body and sperm flagellum. Part of outer dynein arm. Implicated in spermatogenic failure 41. [provided by Alliance of Genome Resources, Apr 2022]

DNAJC9-AS1 (HGNC:31432): (DNAJC9 and MRPS16 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP70	NM_001367801.1	c.3238-5508A>T		intron_variant		ENST00000355577.9	NP_001354730.1
DNAJC9-AS1	NR_038373.1	n.176-10889T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP70	ENST00000355577.9	c.3238-5508A>T		intron_variant		5	NM_001367801.1	ENSP00000347781	P1
DNAJC9-AS1	ENST00000440197.2	n.183-10889T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22801 AN: 150080 Hom.: 2830 Cov.: 30

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0865

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.152 AC: 22845 AN: 150136 Hom.: 2847 Cov.: 30 AF XY: 0.153 AC XY: 11201 AN XY: 73286

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0653

Gnomad4 OTH AF: 0.124

Alfa AF: 0.117 Hom.: 237

Bravo AF: 0.162

Asia WGS AF: 0.260 AC: 901 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.47

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: rs11000566; hg19: chr10-75021682;