X-920280-C-G

Variant names:

• chrX-920280-C-G
• rs5988301

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 0.503 in 151,848 control chromosomes in the GnomAD database, including 19,770 homozygotes. There are 37,468 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 0.50 (19770 hom., 37468 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 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: 0.503 AC: 76278 AN: 151732 Hom.: 19740 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.503 AC: 76358 AN: 151848 Hom.: 19770 Cov.: 32 AF XY: 0.505 AC XY: 37468 AN XY: 74174

African (AFR) AF: 0.622 AC: 25784 AN: 41432

American (AMR) AF: 0.517 AC: 7874 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1917 AN: 3466

East Asian (EAS) AF: 0.502 AC: 2592 AN: 5160

South Asian (SAS) AF: 0.568 AC: 2728 AN: 4800

European-Finnish (FIN) AF: 0.477 AC: 5015 AN: 10510

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28788 AN: 67928

Other (OTH) AF: 0.493 AC: 1040 AN: 2108

Bravo AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.36
DANN	Benign	0.25
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs5988301; hg19: chrX-881015;