rs6768376

chr3-59537812-G-Achr3-59537812-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668131.1(CFAP20DC-DT):n.372+815G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1217+815G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.372+815G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0501

Gnomad4 ASJ AF: 0.0377

Gnomad4 EAS AF: 0.00658

Gnomad4 SAS AF: 0.0260

Gnomad4 FIN AF: 0.0215

Gnomad4 NFE AF: 0.0354

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0397 Hom.: 275

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6768376; hg19: chr3-59523538;