chrX-891455-T-G

Variant names:

• chrX-891455-T-G
• rs5988291

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 0.0896 in 152,070 control chromosomes in the GnomAD database, including 1,587 homozygotes. There are 6,570 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 0.090 (1587 hom., 6570 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 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: 0.0894 AC: 13585 AN: 151952 Hom.: 1578 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0896 AC: 13622 AN: 152070 Hom.: 1587 Cov.: 32 AF XY: 0.0884 AC XY: 6570 AN XY: 74332

African (AFR) AF: 0.262 AC: 10859 AN: 41442

American (AMR) AF: 0.107 AC: 1629 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3470

East Asian (EAS) AF: 0.0330 AC: 170 AN: 5158

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4814

European-Finnish (FIN) AF: 0.0123 AC: 130 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.00697 AC: 474 AN: 68008

Other (OTH) AF: 0.0730 AC: 154 AN: 2110

Bravo AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.27
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs5988291; hg19: chrX-852190;