rs1573036

Variant names:

• chrX-110576840-C-T
• rs1573036

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 0.406 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.407 AC: 44944 AN: 110556 Hom.: 7254 Cov.: 22

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

African (AFR) AF: 0.532 AC: 16139 AN: 30334

American (AMR) AF: 0.283 AC: 2942 AN: 10403

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1207 AN: 2633

East Asian (EAS) AF: 0.0147 AC: 52 AN: 3546

South Asian (SAS) AF: 0.208 AC: 545 AN: 2623

European-Finnish (FIN) AF: 0.381 AC: 2246 AN: 5891

Middle Eastern (MID) AF: 0.330 AC: 71 AN: 215

European-Non Finnish (NFE) AF: 0.394 AC: 20806 AN: 52783

Other (OTH) AF: 0.372 AC: 563 AN: 1513

Alfa AF: 0.392 Hom.: 27094

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1573036; hg19: chrX-109820068;