rs762080

chrX-131400056-C-AchrX-131400056-C-T

Variant summary

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

The XR_938590.3(LOC102723546):n.1999G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 110,438 control chromosomes in the GnomAD database, including 3,515 homozygotes. There are 8,615 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 0.28 (3515 hom., 8615 hem., cov: 23)
• Consequence: LOC102723546 XR_938590.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

Genes affected

LOC102723546 (HGNC:):

IGSF1 (HGNC:5948): (immunoglobulin superfamily member 1) This gene encodes a member of the immunoglobulin-like domain-containing superfamily. Proteins in this superfamily contain varying numbers of immunoglobulin-like domains and are thought to participate in the regulation of interactions between cells. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723546	XR_938590.3	n.1999G>T		non_coding_transcript_exon_variant	1/4
LOC107985705	XR_001755967.2	n.4901+4220C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668852.1	n.309+4220C>A		intron_variant, non_coding_transcript_variant
IGSF1	ENST00000370904.6	c.-912-352G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 30731 AN: 110385 Hom.: 3510 Cov.: 23 AF XY: 0.263 AC XY: 8588 AN XY: 32639

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.279 AC: 30762 AN: 110438 Hom.: 3515 Cov.: 23 AF XY: 0.263 AC XY: 8615 AN XY: 32702

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.285

Alfa AF: 0.0841 Hom.: 362

Bravo AF: 0.275

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.12
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs762080; hg19: chrX-130534030;