X-55157818-A-T

Variant names:

• chrX-55157818-A-T
• rs1874111
• NM_001166701.4:c.120+1311T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166701.4(VCF2):​c.120+1311T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 110,313 control chromosomes in the GnomAD database, including 9,346 homozygotes. There are 15,690 hemizygotes in GnomAD. 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 0.48 (9346 hom., 15690 hem., cov: 22)
• Consequence: VCF2 NM_001166701.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 2 publications found

Genes affected

VCF2 (HGNC:25085): (VCP nuclear cofactor family member 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166701.4. 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
	VCF2	NM_001166701.4	MANE Select	c.120+1311T>A		intron	N/A	NP_001160173.1
	VCF2	NM_001166699.2		c.123+1308T>A		intron	N/A	NP_001160171.1
	VCF2	NM_001166700.2		c.123+1308T>A		intron	N/A	NP_001160172.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VCF2	ENST00000685693.1	MANE Select	c.120+1311T>A		intron	N/A	ENSP00000509111.1
	VCF2	ENST00000332132.8	TSL:1	c.123+1308T>A		intron	N/A	ENSP00000333394.4
	VCF2	ENST00000358460.8	TSL:1	c.120+1311T>A		intron	N/A	ENSP00000364101.3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 52760 AN: 110266 Hom.: 9352 Cov.: 22

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.478 AC: 52775 AN: 110313 Hom.: 9346 Cov.: 22 AF XY: 0.481 AC XY: 15690 AN XY: 32619

African (AFR) AF: 0.336 AC: 10207 AN: 30356

American (AMR) AF: 0.446 AC: 4642 AN: 10399

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1191 AN: 2637

East Asian (EAS) AF: 0.526 AC: 1810 AN: 3444

South Asian (SAS) AF: 0.538 AC: 1388 AN: 2581

European-Finnish (FIN) AF: 0.600 AC: 3478 AN: 5800

Middle Eastern (MID) AF: 0.335 AC: 71 AN: 212

European-Non Finnish (NFE) AF: 0.552 AC: 29097 AN: 52705

Other (OTH) AF: 0.404 AC: 608 AN: 1506

Alfa AF: 0.527 Hom.: 3848

Bravo AF: 0.460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.73
PhyloP100		-0.58
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: rs1874111; hg19: chrX-55184251;