chrX-50901254-C-T

Variant names:

• chrX-50901254-C-T
• rs17249566

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 0.0513 in 111,563 control chromosomes in the GnomAD database, including 158 homozygotes. There are 1,617 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 0.051 (158 hom., 1617 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.071 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: 0.0512 AC: 5713 AN: 111509 Hom.: 158 Cov.: 22

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0145

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0930

Gnomad EAS AF: 0.0101

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0672

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0513 AC: 5718 AN: 111563 Hom.: 158 Cov.: 22 AF XY: 0.0479 AC XY: 1617 AN XY: 33745

African (AFR) AF: 0.0173 AC: 532 AN: 30745

American (AMR) AF: 0.0298 AC: 313 AN: 10500

Ashkenazi Jewish (ASJ) AF: 0.0930 AC: 245 AN: 2633

East Asian (EAS) AF: 0.0102 AC: 36 AN: 3539

South Asian (SAS) AF: 0.0753 AC: 196 AN: 2603

European-Finnish (FIN) AF: 0.0686 AC: 413 AN: 6020

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.0729 AC: 3869 AN: 53088

Other (OTH) AF: 0.0576 AC: 88 AN: 1529

Alfa AF: 0.0708 Hom.: 921

Bravo AF: 0.0465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs17249566; hg19: chrX-50644254;