X-100767972-T-G

Variant names:

• chrX-100767972-T-G
• rs1343216

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 0.338 in 111,521 control chromosomes in the GnomAD database, including 5,646 homozygotes. There are 11,328 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 0.34 (5646 hom., 11328 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.338 AC: 37641 AN: 111464 Hom.: 5644 Cov.: 23

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.338 AC: 37655 AN: 111521 Hom.: 5646 Cov.: 23 AF XY: 0.336 AC XY: 11328 AN XY: 33745

African (AFR) AF: 0.0688 AC: 2132 AN: 30983

American (AMR) AF: 0.369 AC: 3881 AN: 10506

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1412 AN: 2632

East Asian (EAS) AF: 0.625 AC: 2201 AN: 3520

South Asian (SAS) AF: 0.391 AC: 1041 AN: 2663

European-Finnish (FIN) AF: 0.434 AC: 2551 AN: 5880

Middle Eastern (MID) AF: 0.415 AC: 90 AN: 217

European-Non Finnish (NFE) AF: 0.441 AC: 23328 AN: 52913

Other (OTH) AF: 0.380 AC: 580 AN: 1527

Alfa AF: 0.369 Hom.: 2530

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.25
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1343216; hg19: chrX-100022961;