rs4240822

Variant names:

• chrX-71237233-T-A
• rs4240822

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 0.266 in 110,235 control chromosomes in the GnomAD database, including 3,258 homozygotes. There are 8,582 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 0.27 (3258 hom., 8582 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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: 0.266 AC: 29301 AN: 110180 Hom.: 3248 Cov.: 22

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.267

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.266 AC: 29328 AN: 110235 Hom.: 3258 Cov.: 22 AF XY: 0.264 AC XY: 8582 AN XY: 32527

African (AFR) AF: 0.319 AC: 9660 AN: 30294

American (AMR) AF: 0.420 AC: 4348 AN: 10343

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 607 AN: 2628

East Asian (EAS) AF: 0.581 AC: 1989 AN: 3421

South Asian (SAS) AF: 0.363 AC: 926 AN: 2554

European-Finnish (FIN) AF: 0.196 AC: 1154 AN: 5891

Middle Eastern (MID) AF: 0.274 AC: 59 AN: 215

European-Non Finnish (NFE) AF: 0.190 AC: 10007 AN: 52715

Other (OTH) AF: 0.296 AC: 445 AN: 1502

Alfa AF: 0.250 Hom.: 1519

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.5
DANN	Benign	0.83
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4240822; hg19: chrX-70457083;