chrX-920377-G-C

Variant names:

• chrX-920377-G-C
• rs5988494

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 0.635 in 151,928 control chromosomes in the GnomAD database, including 31,541 homozygotes. There are 47,387 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 0.63 (31541 hom., 47387 hem., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96356 AN: 151810 Hom.: 31508 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.635 AC: 96434 AN: 151928 Hom.: 31541 Cov.: 32 AF XY: 0.639 AC XY: 47387 AN XY: 74202

African (AFR) AF: 0.773 AC: 32054 AN: 41466

American (AMR) AF: 0.634 AC: 9684 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2478 AN: 3472

East Asian (EAS) AF: 0.778 AC: 4015 AN: 5158

South Asian (SAS) AF: 0.780 AC: 3762 AN: 4820

European-Finnish (FIN) AF: 0.556 AC: 5851 AN: 10530

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

European-Non Finnish (NFE) AF: 0.538 AC: 36538 AN: 67904

Other (OTH) AF: 0.630 AC: 1329 AN: 2108

Bravo AF: 0.646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.19
DANN	Benign	0.26
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs5988494; hg19: chrX-881112;