X-5578052-G-T

Variant names:

• chrX-5578052-G-T
• rs5961738

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 0.105 in 110,599 control chromosomes in the GnomAD database, including 1,233 homozygotes. There are 3,096 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 0.11 (1233 hom., 3096 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.105 AC: 11643 AN: 110552 Hom.: 1232 Cov.: 23

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.00534

Gnomad EAS AF: 0.00142

Gnomad SAS AF: 0.00792

Gnomad FIN AF: 0.00308

Gnomad MID AF: 0.0213

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.105 AC: 11666 AN: 110599 Hom.: 1233 Cov.: 23 AF XY: 0.0941 AC XY: 3096 AN XY: 32901

African (AFR) AF: 0.328 AC: 9926 AN: 30274

American (AMR) AF: 0.0458 AC: 474 AN: 10347

Ashkenazi Jewish (ASJ) AF: 0.00534 AC: 14 AN: 2624

East Asian (EAS) AF: 0.00142 AC: 5 AN: 3517

South Asian (SAS) AF: 0.00795 AC: 21 AN: 2641

European-Finnish (FIN) AF: 0.00308 AC: 18 AN: 5852

Middle Eastern (MID) AF: 0.0279 AC: 6 AN: 215

European-Non Finnish (NFE) AF: 0.0202 AC: 1067 AN: 52939

Other (OTH) AF: 0.0895 AC: 135 AN: 1509

Alfa AF: 0.0565 Hom.: 873

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.84
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs5961738; hg19: chrX-5496093;