X-146299388-C-T

Variant names:

• chrX-146299388-C-T
• rs4827703

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 0.48 in 110,331 control chromosomes in the GnomAD database, including 9,163 homozygotes. There are 15,728 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 0.48 (9163 hom., 15728 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.584 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: 0.480 AC: 52904 AN: 110281 Hom.: 9160 Cov.: 22

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.480 AC: 52939 AN: 110331 Hom.: 9163 Cov.: 22 AF XY: 0.482 AC XY: 15728 AN XY: 32611

African (AFR) AF: 0.404 AC: 12272 AN: 30360

American (AMR) AF: 0.597 AC: 6220 AN: 10424

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1207 AN: 2629

East Asian (EAS) AF: 0.464 AC: 1602 AN: 3454

South Asian (SAS) AF: 0.398 AC: 1040 AN: 2611

European-Finnish (FIN) AF: 0.606 AC: 3445 AN: 5688

Middle Eastern (MID) AF: 0.378 AC: 79 AN: 209

European-Non Finnish (NFE) AF: 0.495 AC: 26126 AN: 52773

Other (OTH) AF: 0.489 AC: 735 AN: 1503

Alfa AF: 0.470 Hom.: 16481

Bravo AF: 0.485

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.67
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4827703; hg19: chrX-145380906;