rs10514716

Positions:

• chr3-59495862-A-G

Variant summary

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

The ENST00000486137.1(ENSG00000242545):​n.287+14530T>C 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 0.0955 in 151,962 control chromosomes in the GnomAD database, including 735 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 0.095 (735 hom., cov: 32)
• Consequence: ENST00000486137.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

Genes affected

(HGNC:):

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1153-41071A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000486137.1	n.287+14530T>C		intron_variant, non_coding_transcript_variant		3
CFAP20DC-DT	ENST00000668131.1	n.308-41071A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14509 AN: 151844 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.0699

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0916

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0955 AC: 14507 AN: 151962 Hom.: 735 Cov.: 32 AF XY: 0.0942 AC XY: 7005 AN XY: 74346

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0627

Gnomad4 ASJ AF: 0.0699

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0919

Gnomad4 FIN AF: 0.0815

Gnomad4 NFE AF: 0.0882

Gnomad4 OTH AF: 0.0861

Alfa AF: 0.0865 Hom.: 882

Bravo AF: 0.0967

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514716; hg19: chr3-59481588;