rs206037

Variant names:

• chrX-39634466-T-C
• rs206037

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.382 AC: 42569 AN: 111482 Hom.: 6623 Cov.: 23 AF XY: 0.372 AC XY: 12540 AN XY: 33688

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

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.375

Alfa AF: 0.464 Hom.: 12720

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206037; hg19: chrX-39493720;