10-73277101-A-G

Position:

• chr10-73277101-A-G

Variant summary

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

The NM_001367801.1(CFAP70):​c.2730+139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0802 in 1,093,052 control chromosomes in the GnomAD database, including 5,525 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 0.11 (1216 hom., cov: 32)
  • Exomes 𝑓: 0.076 (4309 hom.)
• Consequence: CFAP70 NM_001367801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP70	NM_001367801.1	c.2730+139T>C		intron_variant		ENST00000355577.9	NP_001354730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP70	ENST00000355577.9	c.2730+139T>C		intron_variant		5	NM_001367801.1	ENSP00000347781	P1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15981 AN: 152088 Hom.: 1198 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0952

GnomAD4 exome AF: 0.0762 AC: 71653 AN: 940846 Hom.: 4309 Cov.: 12 AF XY: 0.0795 AC XY: 37213 AN XY: 468286

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.0823

Gnomad4 ASJ exome AF: 0.110

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.208

Gnomad4 FIN exome AF: 0.0452

Gnomad4 NFE exome AF: 0.0565

Gnomad4 OTH exome AF: 0.0872

GnomAD4 genome AF: 0.105 AC: 16047 AN: 152206 Hom.: 1216 Cov.: 32 AF XY: 0.108 AC XY: 8019 AN XY: 74410

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.0856 Hom.: 97

Bravo AF: 0.109

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.4
DANN	Benign	0.60

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: rs3812621; hg19: chr10-75036859;