rs2497935

Variant names:

• chrX-67444424-A-G
• rs2497935

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;