chrX-66021884-G-A

Position:

• chrX-66021884-G-A

Variant summary

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

The NM_007268.3(VSIG4):​c.*379C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 344,982 control chromosomes in the GnomAD database, including 1,844 homozygotes. There are 10,309 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 0.090 (491 hom., 2846 hem., cov: 23)
  • Exomes 𝑓: 0.11 (1353 hom. 7463 hem.)
• Consequence: VSIG4 NM_007268.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VSIG4	NM_007268.3	c.*379C>T		3_prime_UTR_variant	8/8	ENST00000374737.9	NP_009199.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VSIG4	ENST00000374737.9	c.*379C>T		3_prime_UTR_variant	8/8	1	NM_007268.3	ENSP00000363869	P2

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 10024 AN: 111661 Hom.: 492 Cov.: 23 AF XY: 0.0839 AC XY: 2839 AN XY: 33855

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.0748

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00169

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.0938

GnomAD4 exome AF: 0.114 AC: 26497 AN: 233269 Hom.: 1353 Cov.: 4 AF XY: 0.105 AC XY: 7463 AN XY: 71243

Gnomad4 AFR exome AF: 0.0147

Gnomad4 AMR exome AF: 0.0481

Gnomad4 ASJ exome AF: 0.122

Gnomad4 EAS exome AF: 0.000273

Gnomad4 SAS exome AF: 0.0393

Gnomad4 FIN exome AF: 0.141

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.0898 AC: 10029 AN: 111713 Hom.: 491 Cov.: 23 AF XY: 0.0839 AC XY: 2846 AN XY: 33917

Gnomad4 AFR AF: 0.0196

Gnomad4 AMR AF: 0.0581

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00170

Gnomad4 SAS AF: 0.0378

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.130 Hom.: 6637

Bravo AF: 0.0806

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.74

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: rs1044165; hg19: chrX-65241726;