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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP20DC-DT	ENST00000668131.1		n.307+59078A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2279812;

hg19: chr3-59406348;