chrX-146285537-A-G

Variant names:

• chrX-146285537-A-G
• rs910618

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.335 in 110,812 control chromosomes in the GnomAD database, including 4,844 homozygotes. There are 11,009 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 0.34 (4844 hom., 11009 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.483 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: 0.335 AC: 37116 AN: 110759 Hom.: 4837 Cov.: 23

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.335 AC: 37155 AN: 110812 Hom.: 4844 Cov.: 23 AF XY: 0.333 AC XY: 11009 AN XY: 33074

African (AFR) AF: 0.201 AC: 6168 AN: 30661

American (AMR) AF: 0.494 AC: 5119 AN: 10364

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 942 AN: 2629

East Asian (EAS) AF: 0.345 AC: 1201 AN: 3484

South Asian (SAS) AF: 0.334 AC: 886 AN: 2650

European-Finnish (FIN) AF: 0.388 AC: 2282 AN: 5877

Middle Eastern (MID) AF: 0.377 AC: 81 AN: 215

European-Non Finnish (NFE) AF: 0.372 AC: 19630 AN: 52757

Other (OTH) AF: 0.350 AC: 527 AN: 1507

Alfa AF: 0.361 Hom.: 38644

Bravo AF: 0.346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs910618; hg19: chrX-145367055;