chrX-145361034-A-C

Variant names:

• chrX-145361034-A-C
• rs580628

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 0.071 in 111,134 control chromosomes in the GnomAD database, including 242 homozygotes. There are 2,462 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 0.071 (242 hom., 2462 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0914 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: 0.0710 AC: 7890 AN: 111090 Hom.: 241 Cov.: 23

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0513

Gnomad AMR AF: 0.0786

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.148

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0710 AC: 7888 AN: 111134 Hom.: 242 Cov.: 23 AF XY: 0.0738 AC XY: 2462 AN XY: 33358

African (AFR) AF: 0.0174 AC: 535 AN: 30756

American (AMR) AF: 0.0785 AC: 814 AN: 10368

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 245 AN: 2640

East Asian (EAS) AF: 0.0277 AC: 98 AN: 3542

South Asian (SAS) AF: 0.101 AC: 267 AN: 2633

European-Finnish (FIN) AF: 0.149 AC: 880 AN: 5890

Middle Eastern (MID) AF: 0.159 AC: 33 AN: 208

European-Non Finnish (NFE) AF: 0.0917 AC: 4852 AN: 52906

Other (OTH) AF: 0.0855 AC: 129 AN: 1509

Alfa AF: 0.0844 Hom.: 4446

Bravo AF: 0.0642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.67
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs580628; hg19: chrX-144442552;