chrX-920250-T-C

Variant names:

• chrX-920250-T-C
• rs5988299

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 0.643 in 151,830 control chromosomes in the GnomAD database, including 32,518 homozygotes. There are 48,005 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 0.64 (32518 hom., 48005 hem., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97596 AN: 151712 Hom.: 32475 Cov.: 30

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.643 AC: 97688 AN: 151830 Hom.: 32518 Cov.: 30 AF XY: 0.647 AC XY: 48005 AN XY: 74152

African (AFR) AF: 0.802 AC: 33239 AN: 41434

American (AMR) AF: 0.638 AC: 9726 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2473 AN: 3466

East Asian (EAS) AF: 0.785 AC: 4036 AN: 5142

South Asian (SAS) AF: 0.779 AC: 3736 AN: 4794

European-Finnish (FIN) AF: 0.557 AC: 5851 AN: 10510

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36561 AN: 67926

Other (OTH) AF: 0.637 AC: 1343 AN: 2108

Bravo AF: 0.655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.33
DANN	Benign	0.19
PhyloP100		-2.1

Splicing

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

Publications

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Other links and lift over

dbSNP: rs5988299; hg19: chrX-880985;