rs2279812

Positions:

• chr3-59420622-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.307+59078A>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 0.143 in 152,228 control chromosomes in the GnomAD database, including 2,084 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 0.14 (2084 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+59078A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.307+59078A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21807 AN: 152110 Hom.: 2077 Cov.: 32

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.143 AC: 21823 AN: 152228 Hom.: 2084 Cov.: 32 AF XY: 0.146 AC XY: 10895 AN XY: 74420

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.138

Alfa AF: 0.166 Hom.: 1147

Bravo AF: 0.139

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2279812; hg19: chr3-59406348;