rs6654100

chrX-21998020-C-AchrX-21998020-C-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 0.217 in 111,394 control chromosomes in the GnomAD database, including 2,358 homozygotes. There are 6,919 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 0.22 (2358 hom., 6919 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.217 AC: 24140 AN: 111337 Hom.: 2356 Cov.: 23 AF XY: 0.205 AC XY: 6889 AN XY: 33555

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0615

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.217 AC: 24170 AN: 111394 Hom.: 2358 Cov.: 23 AF XY: 0.206 AC XY: 6919 AN XY: 33622

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.194

Alfa AF: 0.0731 Hom.: 338

Bravo AF: 0.224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	8.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6654100; hg19: chrX-22016138; COSMIC: COSV65115559;