ENST00000668131.1:n.263-76887G>T

Variant names:

• chr3-59284613-G-T
• rs17060242
• ENST00000668131.1:n.263-76887G>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.263-76887G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,002 control chromosomes in the GnomAD database, including 3,592 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 0.20 (3592 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 0 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1108-76887G>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.263-76887G>T		intron_variant	Intron 3 of 6
CFAP20DC-DT	ENST00000670321.1	n.403-76887G>T		intron_variant	Intron 3 of 4
CFAP20DC-DT	ENST00000726402.1	n.190+7215G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30605 AN: 151884 Hom.: 3589 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.202 AC: 30640 AN: 152002 Hom.: 3592 Cov.: 32 AF XY: 0.207 AC XY: 15374 AN XY: 74282

African (AFR) AF: 0.186 AC: 7713 AN: 41494

American (AMR) AF: 0.208 AC: 3179 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3466

East Asian (EAS) AF: 0.592 AC: 3037 AN: 5132

South Asian (SAS) AF: 0.318 AC: 1527 AN: 4804

European-Finnish (FIN) AF: 0.183 AC: 1927 AN: 10550

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11939 AN: 67964

Other (OTH) AF: 0.220 AC: 463 AN: 2108

Alfa AF: 0.186 Hom.: 1450

Bravo AF: 0.202

Asia WGS AF: 0.417 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.6
DANN	Benign	0.64
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs17060242; hg19: chr3-59270339;