3-59705846-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.0328

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.161

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510819; hg19: chr3-59691572;