X-117511140-G-C

Variant names:

• chrX-117511140-G-C
• rs5912012

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 0.268 in 110,099 control chromosomes in the GnomAD database, including 2,933 homozygotes. There are 8,783 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 0.27 (2933 hom., 8783 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 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: 0.268 AC: 29475 AN: 110048 Hom.: 2935 Cov.: 22

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.268 AC: 29482 AN: 110099 Hom.: 2933 Cov.: 22 AF XY: 0.269 AC XY: 8783 AN XY: 32653

African (AFR) AF: 0.223 AC: 6793 AN: 30473

American (AMR) AF: 0.317 AC: 3255 AN: 10269

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 597 AN: 2615

East Asian (EAS) AF: 0.466 AC: 1593 AN: 3418

South Asian (SAS) AF: 0.320 AC: 834 AN: 2607

European-Finnish (FIN) AF: 0.294 AC: 1720 AN: 5847

Middle Eastern (MID) AF: 0.178 AC: 38 AN: 213

European-Non Finnish (NFE) AF: 0.268 AC: 14080 AN: 52485

Other (OTH) AF: 0.268 AC: 401 AN: 1495

Alfa AF: 0.163 Hom.: 820

Bravo AF: 0.272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.49
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs5912012; hg19: chrX-116645103;