rs3812621

Variant names:

• chr10-73277101-A-G
• rs3812621
• NM_001367801.1:c.2730+139T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP70	NM_001367801.1	c.2730+139T>C		intron_variant	Intron 22 of 27	ENST00000355577.9	NP_001354730.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP70	ENST00000355577.9	c.2730+139T>C		intron_variant	Intron 22 of 27	5	NM_001367801.1	ENSP00000347781.4

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

African (AFR) AF: 0.155 AC: 3263 AN: 21094

American (AMR) AF: 0.0823 AC: 1832 AN: 22272

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 1690 AN: 15392

East Asian (EAS) AF: 0.278 AC: 8876 AN: 31954

South Asian (SAS) AF: 0.208 AC: 9637 AN: 46266

European-Finnish (FIN) AF: 0.0452 AC: 1407 AN: 31132

Middle Eastern (MID) AF: 0.0684 AC: 234 AN: 3422

European-Non Finnish (NFE) AF: 0.0565 AC: 41139 AN: 728302

Other (OTH) AF: 0.0872 AC: 3575 AN: 41012

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

African (AFR) AF: 0.162 AC: 6736 AN: 41524

American (AMR) AF: 0.0885 AC: 1354 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1567 AN: 5162

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4820

European-Finnish (FIN) AF: 0.0421 AC: 447 AN: 10606

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0610 AC: 4152 AN: 68014

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0885 Hom.: 108

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
PhyloP100		-0.13
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: rs3812621; hg19: chr10-75036859;