rs1910236

chr3-59448694-G-Achr3-59448694-G-C

Variant summary

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

The ENST00000668131.1(CFAP20DC-DT):n.307+87150G>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 0.603 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

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=-0.95).
• 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/exons	MANE	UniProt
CFAP20DC-DT	XR_002959675.2	n.1152+87150G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP20DC-DT	ENST00000668131.1	n.307+87150G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.596

Alfa AF: 0.471 Hom.: 22569

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910236; hg19: chr3-59434420;