rs17358517

chr3-59700006-C-T

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):n.373-36213C>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 0.194 in 152,220 control chromosomes in the GnomAD database, including 3,441 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 0.19 (3441 hom., cov: 33)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1218-109726C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-36213C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29458 AN: 152102 Hom.: 3440 Cov.: 33

Gnomad AFR AF: 0.0769

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.194 AC: 29473 AN: 152220 Hom.: 3441 Cov.: 33 AF XY: 0.196 AC XY: 14618 AN XY: 74416

Gnomad4 AFR AF: 0.0768

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.183

Alfa AF: 0.228 Hom.: 2501

Bravo AF: 0.178

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.2
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17358517; hg19: chr3-59685732;