X-50896828-C-T

Variant names:

• chrX-50896828-C-T
• rs5961228

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 0.215 in 112,033 control chromosomes in the GnomAD database, including 2,715 homozygotes. There are 6,911 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 0.21 (2715 hom., 6911 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.214 AC: 24009 AN: 111982 Hom.: 2707 Cov.: 23

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.215 AC: 24049 AN: 112033 Hom.: 2715 Cov.: 23 AF XY: 0.202 AC XY: 6911 AN XY: 34273

African (AFR) AF: 0.448 AC: 13726 AN: 30649

American (AMR) AF: 0.128 AC: 1376 AN: 10727

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 285 AN: 2655

East Asian (EAS) AF: 0.0368 AC: 130 AN: 3536

South Asian (SAS) AF: 0.168 AC: 450 AN: 2678

European-Finnish (FIN) AF: 0.110 AC: 678 AN: 6186

Middle Eastern (MID) AF: 0.175 AC: 37 AN: 211

European-Non Finnish (NFE) AF: 0.131 AC: 6974 AN: 53169

Other (OTH) AF: 0.198 AC: 305 AN: 1541

Alfa AF: 0.0572 Hom.: 278

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.31
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs5961228; hg19: chrX-50639828;