rs5913038

chrX-79710180-A-GchrX-79710180-A-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 0.183 in 111,120 control chromosomes in the GnomAD database, including 1,597 homozygotes. There are 5,933 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 0.18 (1597 hom., 5933 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 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: 0.183 AC: 20297 AN: 111070 Hom.: 1594 Cov.: 23 AF XY: 0.178 AC XY: 5928 AN XY: 33320

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.183 AC: 20303 AN: 111120 Hom.: 1597 Cov.: 23 AF XY: 0.178 AC XY: 5933 AN XY: 33380

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.188

Alfa AF: 0.196 Hom.: 1379

Bravo AF: 0.198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	4.6
Dann	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5913038; hg19: chrX-78965677;