rs6771019

chr3-59368432-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668131.1(CFAP20DC-DT):n.307+6888G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

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=-0.85).
• 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/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+6888G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.307+6888G>A		intron_variant, non_coding_transcript_variant
CFAP20DC-DT	ENST00000670321.1	n.447+6888G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.701

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.657

Alfa AF: 0.662 Hom.: 6855

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6771019; hg19: chr3-59354158;