rs1394592

Variant names:

• chr3-59625633-A-C
• rs1394592
• ENST00000668131.1:n.372+88636A>C

Your query was ambiguous. Multiple possible variants found:

• chr3-59625633-A-C
• chr3-59625633-A-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.372+88636A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,730 control chromosomes in the GnomAD database, including 7,006 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 0.29 (7006 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 0 publications found

Genes affected

CFAP20DC-DT (HGNC:55618): (CFAP20DC divergent transcript)

ENSG00000299662 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1217+88636A>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.372+88636A>C		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.238+88636A>C		intron_variant	Intron 1 of 1
ENSG00000299662	ENST00000765502.1	n.163+14530T>G		intron_variant	Intron 2 of 2
ENSG00000299662	ENST00000765503.1	n.328-1517T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44578 AN: 151608 Hom.: 6985 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.294 AC: 44628 AN: 151730 Hom.: 7006 Cov.: 32 AF XY: 0.302 AC XY: 22390 AN XY: 74164

African (AFR) AF: 0.287 AC: 11835 AN: 41250

American (AMR) AF: 0.407 AC: 6198 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 802 AN: 3466

East Asian (EAS) AF: 0.492 AC: 2532 AN: 5146

South Asian (SAS) AF: 0.372 AC: 1791 AN: 4818

European-Finnish (FIN) AF: 0.316 AC: 3340 AN: 10562

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17324 AN: 67944

Other (OTH) AF: 0.277 AC: 582 AN: 2104

Alfa AF: 0.155 Hom.: 310

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.076
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1394592; hg19: chr3-59611359;