chr3-59537812-G-A

Variant names:

• chr3-59537812-G-A
• rs6768376
• ENST00000668131.1:n.372+815G>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.372+815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 152,126 control chromosomes in the GnomAD database, including 382 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 0.058 (382 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1217+815G>A		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+815G>A		intron_variant	Intron 5 of 6
CFAP20DC-DT	ENST00000765324.1	n.238+815G>A		intron_variant	Intron 1 of 1
CFAP20DC-DT	ENST00000765325.1	n.294+815G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0577 AC: 8768 AN: 152008 Hom.: 378 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.00656

Gnomad SAS AF: 0.0258

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0578 AC: 8796 AN: 152126 Hom.: 382 Cov.: 32 AF XY: 0.0567 AC XY: 4213 AN XY: 74364

African (AFR) AF: 0.118 AC: 4915 AN: 41506

American (AMR) AF: 0.0501 AC: 765 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.00658 AC: 34 AN: 5170

South Asian (SAS) AF: 0.0260 AC: 125 AN: 4808

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0354 AC: 2405 AN: 67984

Other (OTH) AF: 0.0526 AC: 111 AN: 2110

Alfa AF: 0.0433 Hom.: 778

Bravo AF: 0.0643

Asia WGS AF: 0.0390 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.2
DANN	Benign	0.66
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6768376; hg19: chr3-59523538;