rs2497935

Variant names:

• chrX-67444424-A-G
• rs2497935

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 0.361 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.361 AC: 39828 AN: 110395 Hom.: 9201 Cov.: 22

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

African (AFR) AF: 0.864 AC: 26220 AN: 30350

American (AMR) AF: 0.176 AC: 1831 AN: 10377

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 270 AN: 2621

East Asian (EAS) AF: 0.00200 AC: 7 AN: 3502

South Asian (SAS) AF: 0.0800 AC: 215 AN: 2686

European-Finnish (FIN) AF: 0.177 AC: 1045 AN: 5907

Middle Eastern (MID) AF: 0.255 AC: 55 AN: 216

European-Non Finnish (NFE) AF: 0.184 AC: 9695 AN: 52602

Other (OTH) AF: 0.311 AC: 468 AN: 1504

Alfa AF: 0.261 Hom.: 8390

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.76
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2497935; hg19: chrX-66664266;