X-854145-T-C

Variant names:

• chrX-854145-T-C
• rs5946329

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 0.396 in 151,168 control chromosomes in the GnomAD database, including 14,193 homozygotes. There are 29,015 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 0.40 (14193 hom., 29015 hem., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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: 0.396 AC: 59809 AN: 151044 Hom.: 14167 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.396 AC: 59872 AN: 151168 Hom.: 14193 Cov.: 31 AF XY: 0.393 AC XY: 29015 AN XY: 73870

African (AFR) AF: 0.672 AC: 27750 AN: 41270

American (AMR) AF: 0.339 AC: 5153 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3456

East Asian (EAS) AF: 0.483 AC: 2449 AN: 5074

South Asian (SAS) AF: 0.398 AC: 1907 AN: 4790

European-Finnish (FIN) AF: 0.245 AC: 2582 AN: 10532

Middle Eastern (MID) AF: 0.372 AC: 107 AN: 288

European-Non Finnish (NFE) AF: 0.269 AC: 18186 AN: 67580

Other (OTH) AF: 0.355 AC: 742 AN: 2092

Bravo AF: 0.413

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.74
DANN	Benign	0.13
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs5946329; hg19: chrX-814880;