rs17060242

chr3-59284613-G-T

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):n.263-76887G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,002 control chromosomes in the GnomAD database, including 3,592 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 0.20 (3592 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

Genes affected

CFAP20DC-DT (HGNC:55618): (CFAP20DC divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1108-76887G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.263-76887G>T		intron_variant, non_coding_transcript_variant
CFAP20DC-DT	ENST00000670321.1	n.403-76887G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30605 AN: 151884 Hom.: 3589 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.202 AC: 30640 AN: 152002 Hom.: 3592 Cov.: 32 AF XY: 0.207 AC XY: 15374 AN XY: 74282

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.220

Alfa AF: 0.188 Hom.: 1330

Bravo AF: 0.202

Asia WGS AF: 0.417 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.6
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17060242; hg19: chr3-59270339;