rs36122347

chrX-4986142-C-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 0.141 in 110,481 control chromosomes in the GnomAD database, including 905 homozygotes. There are 4,472 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 0.14 (905 hom., 4472 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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: 0.141 AC: 15548 AN: 110430 Hom.: 902 Cov.: 22 AF XY: 0.137 AC XY: 4471 AN XY: 32726

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.000852

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.0909

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.141 AC: 15557 AN: 110481 Hom.: 905 Cov.: 22 AF XY: 0.136 AC XY: 4472 AN XY: 32787

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0771

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.000854

Gnomad4 SAS AF: 0.0551

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.136

Alfa AF: 0.156 Hom.: 4661

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.16
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36122347; hg19: chrX-4904183;