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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC-DT	ENST00000668131.1		n.373-36213C>T		intron	N/A
	CFAP20DC-DT	ENST00000765324.1		n.239-36213C>T		intron	N/A
	CFAP20DC-DT	ENST00000765326.1		n.146-36213C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17358517;

hg19: chr3-59685732;