Variant chr3-113305155-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001164496.2(CFAP44):c.4759-3C>T variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0221 in 1,536,622 control chromosomes in the GnomAD database, including 476 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 49 hom., cov: 32)

Exomes 𝑓: 0.022 ( 427 hom. )

Consequence

CFAP44
NM_001164496.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.03018

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 5.41

Variant links:

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]

CFAP44 links:

LOC127898559 (HGNC:):

LOC127898559 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 3-113305155-G-A is Benign according to our data. Variant chr3-113305155-G-A is described in ClinVar as [Benign]. Clinvar id is 1267032.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP44	NM_001164496.2 linkuse as main transcript	c.4759-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000393845.9
LOC127898559	NR_183046.1 linkuse as main transcript	n.7395-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP44	ENST00000393845.9 linkuse as main transcript	c.4759-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_001164496.2	P2	Q96MT7-2
CFAP44	ENST00000461734.1 linkuse as main transcript	c.621-3C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0227

AC:

3461

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0240

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0164

Gnomad ASJ

AF:

0.0274

Gnomad EAS

AF:

0.0523

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.0170

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0201

GnomAD3 exomes

AF:

0.0226

AC:

3247

AN:

143488

Hom.:

AF XY:

0.0224

AC XY:

1717

AN XY:

76582

show subpopulations

Gnomad AFR exome

AF:

0.0250

Gnomad AMR exome

AF:

0.0134

Gnomad ASJ exome

AF:

0.0289

Gnomad EAS exome

AF:

0.0505

Gnomad SAS exome

AF:

0.0175

Gnomad FIN exome

AF:

0.0186

Gnomad NFE exome

AF:

0.0223

Gnomad OTH exome

AF:

0.0289

GnomAD4 exome

AF:

0.0221

AC:

30542

AN:

1384328

Hom.:

427

Cov.:

AF XY:

0.0221

AC XY:

15102

AN XY:

683160

show subpopulations

Gnomad4 AFR exome

AF:

0.0255

Gnomad4 AMR exome

AF:

0.0138

Gnomad4 ASJ exome

AF:

0.0280

Gnomad4 EAS exome

AF:

0.0633

Gnomad4 SAS exome

AF:

0.0174

Gnomad4 FIN exome

AF:

0.0176

Gnomad4 NFE exome

AF:

0.0212

Gnomad4 OTH exome

AF:

0.0206

GnomAD4 genome

AF:

0.0227

AC:

3456

AN:

152294

Hom.:

Cov.:

AF XY:

0.0228

AC XY:

1701

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0240

Gnomad4 AMR

AF:

0.0164

Gnomad4 ASJ

AF:

0.0274

Gnomad4 EAS

AF:

0.0525

Gnomad4 SAS

AF:

0.0193

Gnomad4 FIN

AF:

0.0170

Gnomad4 NFE

AF:

0.0220

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.0229

Hom.:

Bravo

AF:

0.0231

Asia WGS

AF:

0.0290

AC:

100

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 25, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.030

dbscSNV1_RF

Benign

0.19

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over