X-140837883-C-T

Variant names:

• chrX-140837883-C-T
• rs1340718

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 110,597 control chromosomes in the GnomAD database, including 3,270 homozygotes. There are 8,462 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 (3270 hom., 8462 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 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: 29630 AN: 110551 Hom.: 3269 Cov.: 23

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.0919

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.268 AC: 29645 AN: 110597 Hom.: 3270 Cov.: 23 AF XY: 0.257 AC XY: 8462 AN XY: 32905

African (AFR) AF: 0.411 AC: 12495 AN: 30407

American (AMR) AF: 0.140 AC: 1454 AN: 10378

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 435 AN: 2638

East Asian (EAS) AF: 0.325 AC: 1138 AN: 3499

South Asian (SAS) AF: 0.273 AC: 714 AN: 2612

European-Finnish (FIN) AF: 0.233 AC: 1355 AN: 5819

Middle Eastern (MID) AF: 0.214 AC: 46 AN: 215

European-Non Finnish (NFE) AF: 0.219 AC: 11585 AN: 52848

Other (OTH) AF: 0.240 AC: 361 AN: 1506

Alfa AF: 0.243 Hom.: 1639

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.0
DANN	Benign	0.60
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1340718; hg19: chrX-139920048;