rs12845178

chrX-16117622-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 0.268 in 109,373 control chromosomes in the GnomAD database, including 3,210 homozygotes. There are 8,169 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 0.27 (3210 hom., 8169 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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: 0.268 AC: 29310 AN: 109324 Hom.: 3216 Cov.: 21 AF XY: 0.258 AC XY: 8164 AN XY: 31686

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.268 AC: 29300 AN: 109373 Hom.: 3210 Cov.: 21 AF XY: 0.257 AC XY: 8169 AN XY: 31745

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.256

Alfa AF: 0.321 Hom.: 18213

Bravo AF: 0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.0
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12845178; hg19: chrX-16135745;