rs6763159

Variant names:

• chr3-59663795-T-C
• rs6763159
• ENST00000668131.1:n.373-72424T>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.373-72424T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,084 control chromosomes in the GnomAD database, including 20,959 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 0.52 (20959 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1217+126798T>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-72424T>C		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.239-72424T>C		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765326.1	n.145+22006T>C		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765327.1	n.213+21087T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78947 AN: 151966 Hom.: 20942 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.519 AC: 79002 AN: 152084 Hom.: 20959 Cov.: 32 AF XY: 0.517 AC XY: 38398 AN XY: 74326

African (AFR) AF: 0.460 AC: 19089 AN: 41474

American (AMR) AF: 0.454 AC: 6937 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2056 AN: 3472

East Asian (EAS) AF: 0.354 AC: 1826 AN: 5154

South Asian (SAS) AF: 0.455 AC: 2193 AN: 4820

European-Finnish (FIN) AF: 0.586 AC: 6194 AN: 10572

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38683 AN: 67988

Other (OTH) AF: 0.537 AC: 1135 AN: 2114

Alfa AF: 0.552 Hom.: 97538

Bravo AF: 0.509

Asia WGS AF: 0.399 AC: 1389 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	0.17
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6763159; hg19: chr3-59649521;