rs6626055

Positions:

• chrX-144544485-A-C
• chrX-144544485-A-T

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 0.0244 in 111,088 control chromosomes in the GnomAD database, including 84 homozygotes. There are 812 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 0.024 (84 hom., 812 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 2717 AN: 111038 Hom.: 85 Cov.: 22 AF XY: 0.0244 AC XY: 813 AN XY: 33314

Gnomad AFR AF: 0.00434

Gnomad AMI AF: 0.0250

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.00607

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00844

Gnomad NFE AF: 0.0259

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0244 AC: 2712 AN: 111088 Hom.: 84 Cov.: 22 AF XY: 0.0243 AC XY: 812 AN XY: 33374

Gnomad4 AFR AF: 0.00433

Gnomad4 AMR AF: 0.0119

Gnomad4 ASJ AF: 0.00607

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0141

Gnomad4 NFE AF: 0.0259

Gnomad4 OTH AF: 0.0237

Alfa AF: 0.0245 Hom.: 644

Bravo AF: 0.0245

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6626055; hg19: chrX-143626006;