X-5578052-G-T

Variant names:

• chrX-5578052-G-T
• rs5961738

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 0.105 in 110,599 control chromosomes in the GnomAD database, including 1,233 homozygotes. There are 3,096 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 0.11 (1233 hom., 3096 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.105 AC: 11643 AN: 110552 Hom.: 1232 Cov.: 23 AF XY: 0.0940 AC XY: 3086 AN XY: 32844

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.00534

Gnomad EAS AF: 0.00142

Gnomad SAS AF: 0.00792

Gnomad FIN AF: 0.00308

Gnomad MID AF: 0.0213

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.105 AC: 11666 AN: 110599 Hom.: 1233 Cov.: 23 AF XY: 0.0941 AC XY: 3096 AN XY: 32901

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.00534

Gnomad4 EAS AF: 0.00142

Gnomad4 SAS AF: 0.00795

Gnomad4 FIN AF: 0.00308

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0454 Hom.: 666

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961738; hg19: chrX-5496093;