3-59705846-C-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.

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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC-DT	ENST00000668131.1		n.373-30373C>G		intron	N/A
	CFAP20DC-DT	ENST00000765324.1		n.239-30373C>G		intron	N/A
	CFAP20DC-DT	ENST00000765326.1		n.146-30373C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10510819;

hg19: chr3-59691572;

COSMIC: COSV107175430;