rs2279812

Variant names:

• chr3-59420622-A-G
• rs2279812
• ENST00000668131.1:n.307+59078A>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.307+59078A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• 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=-0.8).
• 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 rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+59078A>G		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.307+59078A>G		intron_variant	Intron 4 of 6

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

African (AFR) AF: 0.0458 AC: 1905 AN: 41560

American (AMR) AF: 0.170 AC: 2594 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.418 AC: 2151 AN: 5152

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1437 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11394 AN: 68008

Other (OTH) AF: 0.138 AC: 292 AN: 2112

Alfa AF: 0.165 Hom.: 1265

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
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2279812; hg19: chr3-59406348;