X-146305041-G-T

Variant names:

• chrX-146305041-G-T
• rs5920070

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 0.414 in 110,982 control chromosomes in the GnomAD database, including 6,976 homozygotes. There are 13,987 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 0.41 (6976 hom., 13987 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.536 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: 0.414 AC: 45953 AN: 110927 Hom.: 6972 Cov.: 23

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.414 AC: 45994 AN: 110982 Hom.: 6976 Cov.: 23 AF XY: 0.420 AC XY: 13987 AN XY: 33270

African (AFR) AF: 0.295 AC: 9031 AN: 30643

American (AMR) AF: 0.547 AC: 5708 AN: 10427

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1138 AN: 2634

East Asian (EAS) AF: 0.464 AC: 1603 AN: 3453

South Asian (SAS) AF: 0.368 AC: 979 AN: 2663

European-Finnish (FIN) AF: 0.569 AC: 3343 AN: 5879

Middle Eastern (MID) AF: 0.346 AC: 73 AN: 211

European-Non Finnish (NFE) AF: 0.440 AC: 23283 AN: 52870

Other (OTH) AF: 0.437 AC: 668 AN: 1530

Alfa AF: 0.434 Hom.: 15358

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.46
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs5920070; hg19: chrX-145386559;