rs6763159

Positions:

• chr3-59663795-T-C

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):​n.373-72424T>C 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 0.519 in 152,084 control chromosomes in the GnomAD database, including 20,959 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 0.52 (20959 hom., cov: 32)
• Consequence: CFAP20DC-DT ENST00000668131.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP20DC-DT	XR_002959675.2	n.1217+126798T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.373-72424T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78947 AN: 151966 Hom.: 20942 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.519 AC: 79002 AN: 152084 Hom.: 20959 Cov.: 32 AF XY: 0.517 AC XY: 38398 AN XY: 74326

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.537

Alfa AF: 0.560 Hom.: 48620

Bravo AF: 0.509

Asia WGS AF: 0.399 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6763159; hg19: chr3-59649521;