3-113382563-G-A

Position:

• chr3-113382563-G-A

Variant summary

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

The NM_001164496.2(CFAP44):​c.1891-1503C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,838 control chromosomes in the GnomAD database, including 8,989 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 0.34 (8989 hom., cov: 32)
• Consequence: CFAP44 NM_001164496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

CFAP44 (HGNC:25631): (cilia and flagella associated protein 44) Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Apr 2022]

LOC127898559 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP44	NM_001164496.2	c.1891-1503C>T		intron_variant		ENST00000393845.9
LOC127898559	NR_183046.1	n.4851-1503C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP44	ENST00000393845.9	c.1891-1503C>T		intron_variant		5	NM_001164496.2	P2
CFAP44	ENST00000295868.6	c.1891-1503C>T		intron_variant		1		A2
CFAP44	ENST00000488854.6	c.*1307-1503C>T		intron_variant, NMD_transcript_variant		5
CFAP44	ENST00000475568.1	n.509-1503C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51015 AN: 151718 Hom.: 8985 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.336 AC: 51038 AN: 151838 Hom.: 8989 Cov.: 32 AF XY: 0.345 AC XY: 25560 AN XY: 74182

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.323

Alfa AF: 0.284 Hom.: 3635

Bravo AF: 0.328

Asia WGS AF: 0.430 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.38

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: rs1392284; hg19: chr3-113101410;