rs1443936

Variant names:

• chr3-59261439-A-G
• rs1443936
• ENST00000668131.1:n.263-100061A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668131.1(CFAP20DC-DT):​n.263-100061A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,110 control chromosomes in the GnomAD database, including 46,340 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 0.77 (46340 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1108-100061A>G		intron_variant	Intron 4 of 6
CFAP20DC-DT	XR_007095934.1	n.352-15889A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.263-100061A>G		intron_variant	Intron 3 of 6
CFAP20DC-DT	ENST00000670321.1	n.403-100061A>G		intron_variant	Intron 3 of 4
CFAP20DC-DT	ENST00000726402.1	n.120-15889A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117699 AN: 151992 Hom.: 46335 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.774 AC: 117751 AN: 152110 Hom.: 46340 Cov.: 32 AF XY: 0.768 AC XY: 57123 AN XY: 74344

African (AFR) AF: 0.767 AC: 31802 AN: 41478

American (AMR) AF: 0.737 AC: 11261 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2889 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1558 AN: 5166

South Asian (SAS) AF: 0.670 AC: 3226 AN: 4816

European-Finnish (FIN) AF: 0.796 AC: 8418 AN: 10582

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56054 AN: 67998

Other (OTH) AF: 0.769 AC: 1623 AN: 2110

Alfa AF: 0.807 Hom.: 157635

Bravo AF: 0.768

Asia WGS AF: 0.516 AC: 1800 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.8
DANN	Benign	0.76
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1443936; hg19: chr3-59247165;