rs10218356

Variant names:

• chrX-19240194-A-G
• rs10218356

Your query was ambiguous. Multiple possible variants found:

• chrX-19240194-A-G
• chrX-19240194-A-T

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 0.288 in 110,857 control chromosomes in the GnomAD database, including 7,652 homozygotes. There are 8,985 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 0.29 (7652 hom., 8985 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 1 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 = 0.787 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: 0.287 AC: 31850 AN: 110805 Hom.: 7645 Cov.: 21

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.0555

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.160

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.288 AC: 31909 AN: 110857 Hom.: 7652 Cov.: 21 AF XY: 0.271 AC XY: 8985 AN XY: 33129

African (AFR) AF: 0.796 AC: 23975 AN: 30129

American (AMR) AF: 0.225 AC: 2355 AN: 10463

Ashkenazi Jewish (ASJ) AF: 0.0871 AC: 230 AN: 2642

East Asian (EAS) AF: 0.371 AC: 1304 AN: 3511

South Asian (SAS) AF: 0.282 AC: 735 AN: 2606

European-Finnish (FIN) AF: 0.0625 AC: 376 AN: 6013

Middle Eastern (MID) AF: 0.162 AC: 35 AN: 216

European-Non Finnish (NFE) AF: 0.0466 AC: 2476 AN: 53088

Other (OTH) AF: 0.256 AC: 385 AN: 1504

Alfa AF: 0.361 Hom.: 9131

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.62
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs10218356; hg19: chrX-19258312;