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.

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.373-72424T>C		intron	N/A
	CFAP20DC-DT	ENST00000765324.1		n.239-72424T>C		intron	N/A
	CFAP20DC-DT	ENST00000765326.1		n.145+22006T>C		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs6763159;

hg19: chr3-59649521;