rs3732808

Positions:

• chr3-113401767-A-G

Variant summary

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

The NM_001164496.2(CFAP44):​c.1171-28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0649 in 1,576,852 control chromosomes in the GnomAD database, including 3,901 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 0.072 (446 hom., cov: 32)
  • Exomes 𝑓: 0.064 (3455 hom.)
• Consequence: CFAP44 NM_001164496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP44	NM_001164496.2	c.1171-28T>C		intron_variant		ENST00000393845.9	NP_001157968.1
LOC127898559	NR_183046.1	n.4452-28T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP44	ENST00000393845.9	c.1171-28T>C		intron_variant		5	NM_001164496.2	ENSP00000377428	P2
CFAP44	ENST00000295868.6	c.1171-28T>C		intron_variant		1		ENSP00000295868	A2
CFAP44	ENST00000465186.1	c.28-480T>C		intron_variant, NMD_transcript_variant		5		ENSP00000418743
CFAP44	ENST00000488854.6	c.*587-28T>C		intron_variant, NMD_transcript_variant		5		ENSP00000419844

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10951 AN: 152154 Hom.: 445 Cov.: 32

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0898

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0574

GnomAD3 exomes AF: 0.0719 AC: 16048 AN: 223302 Hom.: 731 AF XY: 0.0713 AC XY: 8683 AN XY: 121720

Gnomad AFR exome AF: 0.0929

Gnomad AMR exome AF: 0.0297

Gnomad ASJ exome AF: 0.0881

Gnomad EAS exome AF: 0.164

Gnomad SAS exome AF: 0.0766

Gnomad FIN exome AF: 0.0732

Gnomad NFE exome AF: 0.0626

Gnomad OTH exome AF: 0.0665

GnomAD4 exome AF: 0.0642 AC: 91438 AN: 1424580 Hom.: 3455 Cov.: 29 AF XY: 0.0646 AC XY: 45682 AN XY: 706752

Gnomad4 AFR exome AF: 0.0937

Gnomad4 AMR exome AF: 0.0305

Gnomad4 ASJ exome AF: 0.0858

Gnomad4 EAS exome AF: 0.170

Gnomad4 SAS exome AF: 0.0725

Gnomad4 FIN exome AF: 0.0727

Gnomad4 NFE exome AF: 0.0591

Gnomad4 OTH exome AF: 0.0646

GnomAD4 genome AF: 0.0720 AC: 10967 AN: 152272 Hom.: 446 Cov.: 32 AF XY: 0.0721 AC XY: 5368 AN XY: 74472

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0898

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.0810

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0598

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0703 Hom.: 72

Bravo AF: 0.0723

Asia WGS AF: 0.104 AC: 362 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3732808; hg19: chr3-113120614; COSMIC: COSV55612771; COSMIC: COSV55612771;