chrX-39634466-T-C

Variant names:

• chrX-39634466-T-C
• rs206037

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 0.382 in 111,536 control chromosomes in the GnomAD database, including 6,614 homozygotes. There are 12,545 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 0.38 (6614 hom., 12545 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 4 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 = 0.484 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: 0.382 AC: 42569 AN: 111482 Hom.: 6623 Cov.: 23

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.382 AC: 42554 AN: 111536 Hom.: 6614 Cov.: 23 AF XY: 0.372 AC XY: 12545 AN XY: 33752

African (AFR) AF: 0.190 AC: 5834 AN: 30765

American (AMR) AF: 0.264 AC: 2804 AN: 10628

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 1549 AN: 2641

East Asian (EAS) AF: 0.462 AC: 1631 AN: 3533

South Asian (SAS) AF: 0.316 AC: 848 AN: 2684

European-Finnish (FIN) AF: 0.498 AC: 2950 AN: 5922

Middle Eastern (MID) AF: 0.535 AC: 116 AN: 217

European-Non Finnish (NFE) AF: 0.489 AC: 25906 AN: 52950

Other (OTH) AF: 0.375 AC: 570 AN: 1519

Alfa AF: 0.443 Hom.: 17276

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.75
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs206037; hg19: chrX-39493720;