rs17781597

Variant names:

• chr17-73226699-C-T
• rs17781597
• NM_001098832.2:c.321+466G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098832.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCF1	NM_001098832.2	MANE Select	c.321+466G>A		intron	N/A	NP_001092302.1
	VCF1	NM_032837.3		c.321+466G>A		intron	N/A	NP_116226.2
	VCF1	NM_001289412.2		c.120+466G>A		intron	N/A	NP_001276341.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCF1	ENST00000405159.8	TSL:1 MANE Select	c.321+466G>A		intron	N/A	ENSP00000384832.3
	VCF1	ENST00000403627.7	TSL:1	c.321+466G>A		intron	N/A	ENSP00000384648.3
	VCF1	ENST00000579872.1	TSL:2	c.120+466G>A		intron	N/A	ENSP00000462806.1

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

African (AFR) AF: 0.406 AC: 16855 AN: 41464

American (AMR) AF: 0.483 AC: 7372 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3466

East Asian (EAS) AF: 0.600 AC: 3103 AN: 5168

South Asian (SAS) AF: 0.469 AC: 2258 AN: 4818

European-Finnish (FIN) AF: 0.481 AC: 5080 AN: 10552

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36190 AN: 67960

Other (OTH) AF: 0.498 AC: 1051 AN: 2110

Alfa AF: 0.509 Hom.: 7794

Bravo AF: 0.490

Asia WGS AF: 0.518 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.22
DANN	Benign	0.29
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17781597; hg19: chr17-71222838;