ENST00000668131.1:n.373-30373C>G

Variant names:

• chr3-59705846-C-G
• rs10510819
• ENST00000668131.1:n.373-30373C>G

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):​n.373-30373C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,204 control chromosomes in the GnomAD database, including 2,756 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 0.16 (2756 hom., cov: 33)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1218-103886C>G		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-30373C>G		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.239-30373C>G		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765326.1	n.146-30373C>G		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765327.1	n.214-30373C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24223 AN: 152086 Hom.: 2743 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.160 AC: 24280 AN: 152204 Hom.: 2756 Cov.: 33 AF XY: 0.165 AC XY: 12259 AN XY: 74428

African (AFR) AF: 0.250 AC: 10362 AN: 41506

American (AMR) AF: 0.171 AC: 2608 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 114 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2820 AN: 5172

South Asian (SAS) AF: 0.153 AC: 736 AN: 4814

European-Finnish (FIN) AF: 0.105 AC: 1111 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0904 AC: 6152 AN: 68020

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.125 Hom.: 195

Bravo AF: 0.171

Asia WGS AF: 0.344 AC: 1196 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	12
DANN	Benign	0.69
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10510819; hg19: chr3-59691572; COSMIC: COSV107175430;