3-113361102-G-T

Position:

• chr3-113361102-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS1

The NM_001164496.2(CFAP44):​c.2934+2043C>A variant causes a intron change. The variant allele was found at a frequency of 0.00104 in 207,766 control chromosomes in the GnomAD database, including 2 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 0.00092 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0014 (1 hom.)
• Consequence: CFAP44 NM_001164496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.47

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]

RABGGTBP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00092 (140/152104) while in subpopulation EAS AF= 0.0099 (51/5154). AF 95% confidence interval is 0.00773. There are 1 homozygotes in gnomad4. There are 81 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP44	NM_001164496.2	c.2934+2043C>A		intron_variant		ENST00000393845.9	NP_001157968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP44	ENST00000393845.9	c.2934+2043C>A		intron_variant		5	NM_001164496.2	ENSP00000377428.2
RABGGTBP1	ENST00000462549.1	n.836G>T		non_coding_transcript_exon_variant	1/1	6
CFAP44	ENST00000490481.1	n.165+2043C>A		intron_variant		5		ENSP00000419269.1

Frequencies

GnomAD3 genomes AF: 0.000928 AC: 141 AN: 151986 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.0101

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00398

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000544

Gnomad OTH AF: 0.000957

GnomAD4 exome AF: 0.00138 AC: 77 AN: 55662 Hom.: 1 Cov.: 0 AF XY: 0.00110 AC XY: 35 AN XY: 31930

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000888

Gnomad4 EAS exome AF: 0.00433

Gnomad4 SAS exome AF: 0.000381

Gnomad4 FIN exome AF: 0.00384

Gnomad4 NFE exome AF: 0.000882

Gnomad4 OTH exome AF: 0.00311

GnomAD4 genome AF: 0.000920 AC: 140 AN: 152104 Hom.: 1 Cov.: 31 AF XY: 0.00109 AC XY: 81 AN XY: 74340

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00990

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00398

Gnomad4 NFE AF: 0.000544

Gnomad4 OTH AF: 0.000947

Alfa AF: 0.00144 Hom.: 202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	5.0
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16860868; hg19: chr3-113079949;