rs12845178

Variant names:

• chrX-16117622-C-T
• rs12845178

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;