chrX-16117622-C-T

Variant names:

• chrX-16117622-C-T
• rs12845178

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 29310 AN: 109324 Hom.: 3216 Cov.: 21

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

African (AFR) AF: 0.154 AC: 4593 AN: 29889

American (AMR) AF: 0.284 AC: 2916 AN: 10266

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 859 AN: 2628

East Asian (EAS) AF: 0.138 AC: 489 AN: 3546

South Asian (SAS) AF: 0.248 AC: 630 AN: 2538

European-Finnish (FIN) AF: 0.235 AC: 1331 AN: 5656

Middle Eastern (MID) AF: 0.363 AC: 78 AN: 215

European-Non Finnish (NFE) AF: 0.337 AC: 17669 AN: 52498

Other (OTH) AF: 0.256 AC: 376 AN: 1469

Alfa AF: 0.303 Hom.: 25662

Bravo AF: 0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs12845178; hg19: chrX-16135745;