chrX-51743099-A-C

Variant names:

• chrX-51743099-A-C
• rs11796743

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 0.127 in 111,083 control chromosomes in the GnomAD database, including 799 homozygotes. There are 4,092 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 0.13 (799 hom., 4092 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.127 AC: 14129 AN: 111028 Hom.: 798 Cov.: 23

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.127 AC: 14133 AN: 111083 Hom.: 799 Cov.: 23 AF XY: 0.123 AC XY: 4092 AN XY: 33349

African (AFR) AF: 0.0420 AC: 1287 AN: 30632

American (AMR) AF: 0.110 AC: 1162 AN: 10527

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 340 AN: 2638

East Asian (EAS) AF: 0.0396 AC: 139 AN: 3511

South Asian (SAS) AF: 0.138 AC: 360 AN: 2615

European-Finnish (FIN) AF: 0.187 AC: 1098 AN: 5886

Middle Eastern (MID) AF: 0.168 AC: 36 AN: 214

European-Non Finnish (NFE) AF: 0.179 AC: 9444 AN: 52859

Other (OTH) AF: 0.130 AC: 197 AN: 1520

Alfa AF: 0.158 Hom.: 14217

Bravo AF: 0.120

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		0.073
PromoterAI		0.0048	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11796743; hg19: chrX-51486195;