rs2223841

Variant names:

• chrX-67350329-T-C
• rs2223841

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 0.36 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
• Publications: 5 publications found

ACMG classification

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.360 AC: 39837 AN: 110807 Hom.: 9196 Cov.: 22

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

African (AFR) AF: 0.862 AC: 26168 AN: 30373

American (AMR) AF: 0.176 AC: 1836 AN: 10456

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 271 AN: 2636

East Asian (EAS) AF: 0.00170 AC: 6 AN: 3520

South Asian (SAS) AF: 0.0761 AC: 201 AN: 2641

European-Finnish (FIN) AF: 0.176 AC: 1048 AN: 5954

Middle Eastern (MID) AF: 0.253 AC: 55 AN: 217

European-Non Finnish (NFE) AF: 0.185 AC: 9756 AN: 52873

Other (OTH) AF: 0.312 AC: 471 AN: 1508

Alfa AF: 0.233 Hom.: 21822

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2223841; hg19: chrX-66570171;