X-107355477-A-G

Variant names:

• chrX-107355477-A-G
• rs933315

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 0.332 in 110,632 control chromosomes in the GnomAD database, including 5,731 homozygotes. There are 10,702 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 0.33 (5731 hom., 10702 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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: 0.332 AC: 36679 AN: 110580 Hom.: 5729 Cov.: 22

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.332 AC: 36709 AN: 110632 Hom.: 5731 Cov.: 22 AF XY: 0.325 AC XY: 10702 AN XY: 32914

African (AFR) AF: 0.566 AC: 17106 AN: 30231

American (AMR) AF: 0.464 AC: 4818 AN: 10379

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 814 AN: 2628

East Asian (EAS) AF: 0.604 AC: 2094 AN: 3469

South Asian (SAS) AF: 0.379 AC: 982 AN: 2594

European-Finnish (FIN) AF: 0.114 AC: 684 AN: 6003

Middle Eastern (MID) AF: 0.311 AC: 66 AN: 212

European-Non Finnish (NFE) AF: 0.178 AC: 9444 AN: 52934

Other (OTH) AF: 0.359 AC: 539 AN: 1502

Alfa AF: 0.250 Hom.: 15723

Bravo AF: 0.378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs933315; hg19: chrX-106598707;