3-59372464-T-C

Position:

• chr3-59372464-T-C

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):​n.307+10920T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,748 control chromosomes in the GnomAD database, including 5,663 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 0.27 (5663 hom., cov: 31)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

Genes affected

CFAP20DC-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+10920T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.307+10920T>C		intron_variant
CFAP20DC-DT	ENST00000670321.1	n.448-6493T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40279 AN: 151630 Hom.: 5662 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.266 AC: 40298 AN: 151748 Hom.: 5663 Cov.: 31 AF XY: 0.263 AC XY: 19514 AN XY: 74154

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.283

Alfa AF: 0.299 Hom.: 11588

Bravo AF: 0.271

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11130703; hg19: chr3-59358190;