rs6771019

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.

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.307+6888G>A		intron	N/A
	CFAP20DC-DT	ENST00000670321.1		n.447+6888G>A		intron	N/A
	CFAP20DC-DT	ENST00000726402.1		n.235+6888G>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs6771019;

hg19: chr3-59354158;