rs17358517

Variant names:

• chr3-59700006-C-T
• rs17358517
• ENST00000668131.1:n.373-36213C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668131.1(CFAP20DC-DT):​n.373-36213C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1218-109726C>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-36213C>T		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.239-36213C>T		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765326.1	n.146-36213C>T		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765327.1	n.214-36213C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0768 AC: 3190 AN: 41550

American (AMR) AF: 0.197 AC: 3014 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.143 AC: 740 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1188 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3370 AN: 10584

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16779 AN: 68006

Other (OTH) AF: 0.183 AC: 386 AN: 2110

Alfa AF: 0.228 Hom.: 2720

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
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs17358517; hg19: chr3-59685732;