rs1443936

Positions:

• chr3-59261439-A-G

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):​n.263-100061A>G 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 0.774 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574

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=-0.82).
• 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/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1108-100061A>G		intron_variant, non_coding_transcript_variant
CFAP20DC-DT	XR_007095934.1	n.352-15889A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.263-100061A>G		intron_variant, non_coding_transcript_variant
CFAP20DC-DT	ENST00000670321.1	n.403-100061A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.769

Alfa AF: 0.815 Hom.: 66106

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1443936; hg19: chr3-59247165;