3-59658507-G-T

Variant names:

• chr3-59658507-G-T
• rs2121794
• ENST00000668131.1:n.373-77712G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000668131.1(CFAP20DC-DT):​n.373-77712G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 3 publications found

Genes affected

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

ENSG00000299662 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1217+121510G>T		intron_variant	Intron 6 of 6
LOC339902	NR_149028.1	n.-10C>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-77712G>T		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.239-77712G>T		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765326.1	n.145+16718G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 112001

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.38
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2121794; hg19: chr3-59644233;