chrX-110576840-C-T

Variant names:

• chrX-110576840-C-T
• rs1573036

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 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 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;