rs5941436

Variant names:

• chrX-90033228-C-A
• rs5941436

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 0.164 in 108,282 control chromosomes in the GnomAD database, including 1,333 homozygotes. There are 4,940 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 0.16 (1333 hom., 4940 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 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: 0.165 AC: 17816 AN: 108242 Hom.: 1337 Cov.: 22

Gnomad AFR AF: 0.0714

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.164 AC: 17811 AN: 108282 Hom.: 1333 Cov.: 22 AF XY: 0.159 AC XY: 4940 AN XY: 30972

African (AFR) AF: 0.0714 AC: 2133 AN: 29892

American (AMR) AF: 0.121 AC: 1216 AN: 10027

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 672 AN: 2605

East Asian (EAS) AF: 0.289 AC: 982 AN: 3400

South Asian (SAS) AF: 0.283 AC: 716 AN: 2528

European-Finnish (FIN) AF: 0.159 AC: 843 AN: 5314

Middle Eastern (MID) AF: 0.248 AC: 51 AN: 206

European-Non Finnish (NFE) AF: 0.207 AC: 10770 AN: 52139

Other (OTH) AF: 0.164 AC: 246 AN: 1497

Alfa AF: 0.189 Hom.: 11382

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs5941436; hg19: chrX-89288227;