X-136660841-C-T

Variant names:

• chrX-136660841-C-T
• rs3092921

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 0.259 in 110,297 control chromosomes in the GnomAD database, including 5,505 homozygotes. There are 7,832 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 0.26 (5505 hom., 7832 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 28570 AN: 110245 Hom.: 5503 Cov.: 22

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.00438

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.0853

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.259 AC: 28611 AN: 110297 Hom.: 5505 Cov.: 22 AF XY: 0.240 AC XY: 7832 AN XY: 32583

African (AFR) AF: 0.674 AC: 20201 AN: 29955

American (AMR) AF: 0.174 AC: 1824 AN: 10458

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 357 AN: 2622

East Asian (EAS) AF: 0.101 AC: 354 AN: 3514

South Asian (SAS) AF: 0.226 AC: 570 AN: 2523

European-Finnish (FIN) AF: 0.0649 AC: 387 AN: 5967

Middle Eastern (MID) AF: 0.230 AC: 49 AN: 213

European-Non Finnish (NFE) AF: 0.0853 AC: 4507 AN: 52860

Other (OTH) AF: 0.239 AC: 359 AN: 1500

Alfa AF: 0.160 Hom.: 16131

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.74
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3092921; hg19: chrX-135743000;