chrX-51467205-C-T

Variant names:

• chrX-51467205-C-T
• rs1327301

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 0.29 in 110,990 control chromosomes in the GnomAD database, including 3,632 homozygotes. There are 9,390 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 0.29 (3632 hom., 9390 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.290 AC: 32135 AN: 110935 Hom.: 3635 Cov.: 23

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.290 AC: 32133 AN: 110990 Hom.: 3632 Cov.: 23 AF XY: 0.282 AC XY: 9390 AN XY: 33272

African (AFR) AF: 0.206 AC: 6320 AN: 30610

American (AMR) AF: 0.197 AC: 2070 AN: 10508

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 644 AN: 2635

East Asian (EAS) AF: 0.0773 AC: 272 AN: 3518

South Asian (SAS) AF: 0.267 AC: 694 AN: 2604

European-Finnish (FIN) AF: 0.409 AC: 2392 AN: 5853

Middle Eastern (MID) AF: 0.310 AC: 66 AN: 213

European-Non Finnish (NFE) AF: 0.359 AC: 18982 AN: 52858

Other (OTH) AF: 0.272 AC: 414 AN: 1521

Alfa AF: 0.333 Hom.: 35278

Bravo AF: 0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.6
DANN	Benign	0.85
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs1327301; hg19: chrX-51210057;