chr3-59368432-G-A

Variant names:

• chr3-59368432-G-A
• rs6771019
• ENST00000668131.1:n.307+6888G>A

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+6888G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,692 control chromosomes in the GnomAD database, including 28,647 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 0.60 (28647 hom., cov: 31)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+6888G>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+6888G>A		intron_variant	Intron 4 of 6
CFAP20DC-DT	ENST00000670321.1	n.447+6888G>A		intron_variant	Intron 4 of 4
CFAP20DC-DT	ENST00000726402.1	n.235+6888G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91556 AN: 151574 Hom.: 28635 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.604 AC: 91605 AN: 151692 Hom.: 28647 Cov.: 31 AF XY: 0.601 AC XY: 44513 AN XY: 74086

African (AFR) AF: 0.453 AC: 18738 AN: 41386

American (AMR) AF: 0.701 AC: 10695 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2611 AN: 3458

East Asian (EAS) AF: 0.347 AC: 1777 AN: 5128

South Asian (SAS) AF: 0.638 AC: 3074 AN: 4820

European-Finnish (FIN) AF: 0.592 AC: 6218 AN: 10498

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.683 AC: 46369 AN: 67848

Other (OTH) AF: 0.657 AC: 1386 AN: 2108

Alfa AF: 0.649 Hom.: 49799

Bravo AF: 0.604

Asia WGS AF: 0.514 AC: 1790 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.76
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6771019; hg19: chr3-59354158;