rs1291993

Variant names:

• chrX-127221560-G-T
• rs275978

Your query was ambiguous. Multiple possible variants found:

• chrX-127221560-G-T
• chrX-127221560-G-C

Variant summary

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

The variant allele was found at a frequency of 0.289 in 109,818 control chromosomes in the GnomAD database, including 3,725 homozygotes. There are 9,125 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 (3725 hom., 9125 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

ACMG classification

Verdict is Benign. Variant got -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 = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.289 AC: 31686 AN: 109767 Hom.: 3726 Cov.: 22 AF XY: 0.284 AC XY: 9113 AN XY: 32087

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.289 AC: 31699 AN: 109818 Hom.: 3725 Cov.: 22 AF XY: 0.284 AC XY: 9125 AN XY: 32148

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.283

Alfa AF: 0.118 Hom.: 555

Bravo AF: 0.307

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275978; hg19: chrX-126355543;