3-59705999-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1218-103733G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-30220G>A		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.239-30220G>A		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765326.1	n.146-30220G>A		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765327.1	n.214-30220G>A		intron_variant	Intron 2 of 2

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 v4.3

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;