rs5977968

chrX-134189815-T-C

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 0.189 in 111,301 control chromosomes in the GnomAD database, including 1,900 homozygotes. There are 6,338 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 0.19 (1900 hom., 6338 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.189 AC: 21037 AN: 111251 Hom.: 1898 Cov.: 23 AF XY: 0.188 AC XY: 6313 AN XY: 33497

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.189 AC: 21064 AN: 111301 Hom.: 1900 Cov.: 23 AF XY: 0.189 AC XY: 6338 AN XY: 33557

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.0985

Gnomad4 NFE AF: 0.0919

Gnomad4 OTH AF: 0.181

Alfa AF: 0.135 Hom.: 2600

Bravo AF: 0.223

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.1
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5977968; hg19: chrX-133323845;