rs6627057

chrX-145059799-T-G

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 0.158 in 112,475 control chromosomes in the GnomAD database, including 1,122 homozygotes. There are 5,251 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 0.16 (1122 hom., 5251 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

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 (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.158 AC: 17772 AN: 112425 Hom.: 1121 Cov.: 24 AF XY: 0.151 AC XY: 5237 AN XY: 34601

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0131

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.110

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.158 AC: 17779 AN: 112475 Hom.: 1122 Cov.: 24 AF XY: 0.151 AC XY: 5251 AN XY: 34661

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.160

Alfa AF: 0.131 Hom.: 7111

Bravo AF: 0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.6
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6627057; hg19: chrX-144141319;