rs1573036

chrX-110576840-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.406 in 110,610 control chromosomes in the GnomAD database, including 7,249 homozygotes. There are 12,654 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 0.41 (7249 hom., 12654 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.407 AC: 44944 AN: 110556 Hom.: 7254 Cov.: 22 AF XY: 0.384 AC XY: 12636 AN XY: 32866

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.406 AC: 44954 AN: 110610 Hom.: 7249 Cov.: 22 AF XY: 0.384 AC XY: 12654 AN XY: 32930

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.372

Alfa AF: 0.381 Hom.: 19969

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	5.2
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1573036; hg19: chrX-109820068;