rs17781597

Positions:

• chr17-73226699-C-T

Variant summary

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

The NM_001098832.2(VCF1):​c.321+466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,006 control chromosomes in the GnomAD database, including 18,363 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 0.49 (18363 hom., cov: 32)
• Consequence: VCF1 NM_001098832.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

VCF1 (HGNC:25918): (VCP nuclear cofactor family member 1)

FAM104A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VCF1	NM_001098832.2	c.321+466G>A		intron_variant		ENST00000405159.8	NP_001092302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM104A	ENST00000405159.8	c.321+466G>A		intron_variant		1	NM_001098832.2	ENSP00000384832.3

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74046 AN: 151888 Hom.: 18354 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.487 AC: 74094 AN: 152006 Hom.: 18363 Cov.: 32 AF XY: 0.485 AC XY: 35998 AN XY: 74276

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.498

Alfa AF: 0.512 Hom.: 6267

Bravo AF: 0.490

Asia WGS AF: 0.518 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17781597; hg19: chr17-71222838;