rs2121794

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-59658507-G-A
• chr3-59658507-G-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.373-77712G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,830 control chromosomes in the GnomAD database, including 36,791 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 0.69 (36791 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105069 AN: 151714 Hom.: 36759 Cov.: 30

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.693 AC: 105144 AN: 151830 Hom.: 36791 Cov.: 30 AF XY: 0.692 AC XY: 51304 AN XY: 74182

African (AFR) AF: 0.690 AC: 28540 AN: 41386

American (AMR) AF: 0.585 AC: 8934 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2394 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2745 AN: 5114

South Asian (SAS) AF: 0.610 AC: 2928 AN: 4800

European-Finnish (FIN) AF: 0.792 AC: 8351 AN: 10540

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48866 AN: 67936

Other (OTH) AF: 0.690 AC: 1457 AN: 2112

Alfa AF: 0.701 Hom.: 112001

Bravo AF: 0.676

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.32
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;