rs6627057

Variant names:

• chrX-145059799-T-G
• rs6627057

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.158 AC: 17772 AN: 112425 Hom.: 1121 Cov.: 24

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

African (AFR) AF: 0.224 AC: 6920 AN: 30924

American (AMR) AF: 0.182 AC: 1944 AN: 10688

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 373 AN: 2647

East Asian (EAS) AF: 0.267 AC: 940 AN: 3519

South Asian (SAS) AF: 0.147 AC: 408 AN: 2769

European-Finnish (FIN) AF: 0.130 AC: 808 AN: 6233

Middle Eastern (MID) AF: 0.102 AC: 22 AN: 216

European-Non Finnish (NFE) AF: 0.115 AC: 6108 AN: 53251

Other (OTH) AF: 0.160 AC: 247 AN: 1543

Alfa AF: 0.141 Hom.: 10873

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs6627057; hg19: chrX-144141319;