chr3-59705999-G-A

Variant names:

• chr3-59705999-G-A
• rs17061085
• ENST00000668131.1:n.373-30220G>A

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):​n.373-30220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 152,304 control chromosomes in the GnomAD database, including 836 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 0.096 (836 hom., cov: 33)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC-DT	ENST00000668131.1		n.373-30220G>A		intron	N/A
	CFAP20DC-DT	ENST00000765324.1		n.239-30220G>A		intron	N/A
	CFAP20DC-DT	ENST00000765326.1		n.146-30220G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14615 AN: 152186 Hom.: 837 Cov.: 33

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0985

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

GnomAD4 genome AF: 0.0959 AC: 14611 AN: 152304 Hom.: 836 Cov.: 33 AF XY: 0.100 AC XY: 7446 AN XY: 74462

African (AFR) AF: 0.0393 AC: 1632 AN: 41570

American (AMR) AF: 0.104 AC: 1590 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.127 AC: 659 AN: 5188

South Asian (SAS) AF: 0.213 AC: 1030 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1509 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7535 AN: 68026

Other (OTH) AF: 0.0974 AC: 206 AN: 2114

Alfa AF: 0.0921 Hom.: 118

Bravo AF: 0.0890

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.67
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs17061085; hg19: chr3-59691725;