chrX-102009826-C-T

Variant names:

• chrX-102009826-C-T
• rs5944811

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 0.125 in 110,411 control chromosomes in the GnomAD database, including 881 homozygotes. There are 3,890 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 0.12 (881 hom., 3890 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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: 0.125 AC: 13775 AN: 110363 Hom.: 881 Cov.: 22

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.0497

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00140

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.125 AC: 13772 AN: 110411 Hom.: 881 Cov.: 22 AF XY: 0.118 AC XY: 3890 AN XY: 32879

African (AFR) AF: 0.0344 AC: 1054 AN: 30657

American (AMR) AF: 0.0998 AC: 1032 AN: 10336

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 419 AN: 2624

East Asian (EAS) AF: 0.00140 AC: 5 AN: 3563

South Asian (SAS) AF: 0.0365 AC: 96 AN: 2631

European-Finnish (FIN) AF: 0.216 AC: 1245 AN: 5775

Middle Eastern (MID) AF: 0.178 AC: 38 AN: 214

European-Non Finnish (NFE) AF: 0.184 AC: 9662 AN: 52431

Other (OTH) AF: 0.125 AC: 187 AN: 1496

Alfa AF: 0.149 Hom.: 963

Bravo AF: 0.116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs5944811; hg19: chrX-101264799;