X-120469781-T-G

Variant names:

• chrX-120469781-T-G
• rs42900

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 0.304 in 108,309 control chromosomes in the GnomAD database, including 4,416 homozygotes. There are 8,689 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 0.30 (4416 hom., 8689 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 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: 0.303 AC: 32848 AN: 108256 Hom.: 4402 Cov.: 21

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.304 AC: 32907 AN: 108309 Hom.: 4416 Cov.: 21 AF XY: 0.283 AC XY: 8689 AN XY: 30749

African (AFR) AF: 0.472 AC: 13955 AN: 29536

American (AMR) AF: 0.414 AC: 4157 AN: 10049

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 525 AN: 2616

East Asian (EAS) AF: 0.394 AC: 1334 AN: 3388

South Asian (SAS) AF: 0.283 AC: 706 AN: 2497

European-Finnish (FIN) AF: 0.114 AC: 638 AN: 5589

Middle Eastern (MID) AF: 0.196 AC: 41 AN: 209

European-Non Finnish (NFE) AF: 0.210 AC: 10959 AN: 52302

Other (OTH) AF: 0.304 AC: 444 AN: 1461

Alfa AF: 0.252 Hom.: 1559

Bravo AF: 0.342

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.79
PhyloP100		-0.51
PromoterAI		-0.048	Neutral

Splicing

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

Other links and lift over

dbSNP: rs42900; hg19: chrX-119603636;