rs6783485

Variant names:

• chr3-59442071-G-A
• rs6783485
• ENST00000668131.1:n.307+80527G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-59442071-G-A
• chr3-59442071-G-C

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):​n.307+80527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.049 in 152,160 control chromosomes in the GnomAD database, including 322 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 0.049 (322 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+80527G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.307+80527G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 7437 AN: 152042 Hom.: 321 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.0440

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

GnomAD4 genome AF: 0.0490 AC: 7456 AN: 152160 Hom.: 322 Cov.: 32 AF XY: 0.0491 AC XY: 3652 AN XY: 74378

African (AFR) AF: 0.115 AC: 4784 AN: 41466

American (AMR) AF: 0.0426 AC: 651 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.0264 AC: 137 AN: 5188

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4822

European-Finnish (FIN) AF: 0.0337 AC: 357 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0182 AC: 1237 AN: 68010

Other (OTH) AF: 0.0492 AC: 104 AN: 2114

Alfa AF: 0.0282 Hom.: 174

Bravo AF: 0.0530

Asia WGS AF: 0.0570 AC: 196 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	0.010
DANN	Benign	0.71
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs6783485; hg19: chr3-59427797;