rs2223841

Positions:

• chrX-67350329-T-C

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 0.36 in 110,859 control chromosomes in the GnomAD database, including 9,204 homozygotes. There are 11,074 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 0.36 (9204 hom., 11074 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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: 0.360 AC: 39837 AN: 110807 Hom.: 9196 Cov.: 22 AF XY: 0.333 AC XY: 11027 AN XY: 33087

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00170

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.360 AC: 39896 AN: 110859 Hom.: 9204 Cov.: 22 AF XY: 0.334 AC XY: 11074 AN XY: 33149

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.00170

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.312

Alfa AF: 0.202 Hom.: 11198

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2223841; hg19: chrX-66570171;