rs2497935

chrX-67444424-A-G

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 0.361 in 110,446 control chromosomes in the GnomAD database, including 9,211 homozygotes. There are 11,113 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 (9211 hom., 11113 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 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: 0.361 AC: 39828 AN: 110395 Hom.: 9201 Cov.: 22 AF XY: 0.337 AC XY: 11065 AN XY: 32869

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.00199

Gnomad SAS AF: 0.0805

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.361 AC: 39890 AN: 110446 Hom.: 9211 Cov.: 22 AF XY: 0.337 AC XY: 11113 AN XY: 32930

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.00200

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.311

Alfa AF: 0.253 Hom.: 3320

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.78
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: rs2497935; hg19: chrX-66664266;