rs4240822

chrX-71237233-T-A

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 0.266 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.266 AC: 29301 AN: 110180 Hom.: 3248 Cov.: 22 AF XY: 0.264 AC XY: 8558 AN XY: 32462

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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.296

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4240822; hg19: chrX-70457083;