X-23687058-T-C

Variant names:

• chrX-23687058-T-C
• rs477233

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 0.426 in 109,640 control chromosomes in the GnomAD database, including 7,274 homozygotes. There are 13,299 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 0.43 (7274 hom., 13299 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.426 AC: 46726 AN: 109586 Hom.: 7280 Cov.: 22

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.426 AC: 46742 AN: 109640 Hom.: 7274 Cov.: 22 AF XY: 0.416 AC XY: 13299 AN XY: 31984

African (AFR) AF: 0.421 AC: 12743 AN: 30245

American (AMR) AF: 0.477 AC: 4812 AN: 10092

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1353 AN: 2624

East Asian (EAS) AF: 0.501 AC: 1715 AN: 3423

South Asian (SAS) AF: 0.336 AC: 888 AN: 2644

European-Finnish (FIN) AF: 0.411 AC: 2292 AN: 5571

Middle Eastern (MID) AF: 0.531 AC: 113 AN: 213

European-Non Finnish (NFE) AF: 0.415 AC: 21889 AN: 52683

Other (OTH) AF: 0.448 AC: 662 AN: 1479

Alfa AF: 0.430 Hom.: 54719

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.5
DANN	Benign	0.89
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs477233; hg19: chrX-23705175;