3-59448694-G-A

Variant names:

• chr3-59448694-G-A
• rs1910236
• ENST00000668131.1:n.307+87150G>A

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+87150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,048 control chromosomes in the GnomAD database, including 30,325 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 0.60 (30325 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+87150G>A		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+87150G>A		intron_variant	Intron 4 of 6
CFAP20DC-DT	ENST00000765325.1	n.79+899G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91618 AN: 151930 Hom.: 30253 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.603 AC: 91748 AN: 152048 Hom.: 30325 Cov.: 32 AF XY: 0.603 AC XY: 44838 AN XY: 74324

African (AFR) AF: 0.867 AC: 35977 AN: 41506

American (AMR) AF: 0.604 AC: 9232 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4600 AN: 5160

South Asian (SAS) AF: 0.489 AC: 2359 AN: 4822

European-Finnish (FIN) AF: 0.459 AC: 4841 AN: 10542

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.461 AC: 31315 AN: 67950

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.512 Hom.: 67570

Bravo AF: 0.631

Asia WGS AF: 0.720 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1910236; hg19: chr3-59434420;