3-58867813-A-C

Position:

• chr3-58867813-A-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Moderate BP6_Moderate

The NM_001394063.1(CFAP20DC):​c.1135+4T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0041 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CFAP20DC NM_001394063.1 splice_region, intron
• Scores: Splicing: ADA: 0.0003144
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0250

Genes affected

CFAP20DC (HGNC:24763): (CFAP20 domain containing)

CFAP20DC-AS1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BP6: Variant 3-58867813-A-C is Benign according to our data. Variant chr3-58867813-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2653922.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP20DC	NM_001394063.1	c.1135+4T>G		splice_region_variant, intron_variant		ENST00000482387.7	NP_001380992.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP20DC	ENST00000482387.7	c.1135+4T>G		splice_region_variant, intron_variant		5	NM_001394063.1	ENSP00000417122.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 38 AN: 152046 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.000625

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00413 AC: 5964 AN: 1444996 Hom.: 0 Cov.: 30 AF XY: 0.00395 AC XY: 2843 AN XY: 719450

Gnomad4 AFR exome AF: 0.00326

Gnomad4 AMR exome AF: 0.000627

Gnomad4 ASJ exome AF: 0.00270

Gnomad4 EAS exome AF: 0.00284

Gnomad4 SAS exome AF: 0.00136

Gnomad4 FIN exome AF: 0.00152

Gnomad4 NFE exome AF: 0.00473

Gnomad4 OTH exome AF: 0.00401

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000243 AC: 37 AN: 152164 Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20 AN XY: 74378

Gnomad4 AFR AF: 0.0000962

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000968

Gnomad4 SAS AF: 0.000626

Gnomad4 FIN AF: 0.000754

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2023

CFAP20DC: BP4 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	9.3
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00031
dbscSNV1_RF	Benign	0.13
SpliceAI score (max)		0.090		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: rs2079821130; hg19: chr3-58853539;