rs6627483

Variant names:

• chrX-151870250-C-T
• rs6627483

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 0.112 in 111,891 control chromosomes in the GnomAD database, including 647 homozygotes. There are 3,754 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 0.11 (647 hom., 3754 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 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: 0.112 AC: 12535 AN: 111837 Hom.: 651 Cov.: 23

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.112 AC: 12521 AN: 111891 Hom.: 647 Cov.: 23 AF XY: 0.110 AC XY: 3754 AN XY: 34093

African (AFR) AF: 0.0232 AC: 718 AN: 30923

American (AMR) AF: 0.110 AC: 1158 AN: 10538

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 459 AN: 2643

East Asian (EAS) AF: 0.125 AC: 443 AN: 3531

South Asian (SAS) AF: 0.0820 AC: 222 AN: 2706

European-Finnish (FIN) AF: 0.155 AC: 937 AN: 6049

Middle Eastern (MID) AF: 0.219 AC: 47 AN: 215

European-Non Finnish (NFE) AF: 0.154 AC: 8173 AN: 53106

Other (OTH) AF: 0.155 AC: 233 AN: 1503

Alfa AF: 0.142 Hom.: 9633

Bravo AF: 0.108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.74
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs6627483; hg19: chrX-151038722;