rs5964486

chrX-66024220-T-C

Variant summary

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

The NM_007268.3(VSIG4):c.940+805A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 111,711 control chromosomes in the GnomAD database, including 5,426 homozygotes. There are 9,195 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 0.29 (5426 hom., 9195 hem., cov: 23)
• Consequence: VSIG4 NM_007268.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

Genes affected

VSIG4 (HGNC:17032): (V-set and immunoglobulin domain containing 4) This gene encodes a v-set and immunoglobulin-domain containing protein that is structurally related to the B7 family of immune regulatory proteins. The encoded protein may be a negative regulator of T-cell responses. This protein is also a receptor for the complement component 3 fragments C3b and iC3b. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VSIG4	NM_007268.3	c.940+805A>G		intron_variant		ENST00000374737.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VSIG4	ENST00000374737.9	c.940+805A>G		intron_variant		1	NM_007268.3	P2

Frequencies

GnomAD3 genomes AF: 0.289 AC: 32264 AN: 111658 Hom.: 5425 Cov.: 23 AF XY: 0.270 AC XY: 9149 AN XY: 33882

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.000556

Gnomad SAS AF: 0.0889

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.289 AC: 32310 AN: 111711 Hom.: 5426 Cov.: 23 AF XY: 0.271 AC XY: 9195 AN XY: 33945

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.000558

Gnomad4 SAS AF: 0.0914

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.232

Alfa AF: 0.189 Hom.: 3793

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.31
Dann	Benign	0.53

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: rs5964486; hg19: chrX-65244062;