X-30269140-A-G

Variant names:

• chrX-30269140-A-G
• rs10521956

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 0.399 in 109,800 control chromosomes in the GnomAD database, including 6,684 homozygotes. There are 12,265 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 0.40 (6684 hom., 12265 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.399 AC: 43775 AN: 109748 Hom.: 6685 Cov.: 22

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.399 AC: 43802 AN: 109800 Hom.: 6684 Cov.: 22 AF XY: 0.382 AC XY: 12265 AN XY: 32148

African (AFR) AF: 0.368 AC: 11154 AN: 30287

American (AMR) AF: 0.386 AC: 3971 AN: 10283

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 889 AN: 2623

East Asian (EAS) AF: 0.0329 AC: 115 AN: 3498

South Asian (SAS) AF: 0.218 AC: 563 AN: 2578

European-Finnish (FIN) AF: 0.462 AC: 2650 AN: 5730

Middle Eastern (MID) AF: 0.316 AC: 67 AN: 212

European-Non Finnish (NFE) AF: 0.452 AC: 23683 AN: 52415

Other (OTH) AF: 0.354 AC: 531 AN: 1502

Alfa AF: 0.406 Hom.: 3250

Bravo AF: 0.391

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10521956; hg19: chrX-30287257;