rs3131301

Positions:

• chrX-51573615-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0229 in 111,997 control chromosomes in the GnomAD database, including 33 homozygotes. There are 770 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 0.023 (33 hom., 770 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0229 (2563/111997) while in subpopulation NFE AF= 0.0358 (1903/53208). AF 95% confidence interval is 0.0344. There are 33 homozygotes in gnomad4. There are 770 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 33 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.51573615A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0229 AC: 2564 AN: 111952 Hom.: 33 Cov.: 23 AF XY: 0.0226 AC XY: 771 AN XY: 34106

Gnomad AFR AF: 0.00480

Gnomad AMI AF: 0.0543

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.00945

Gnomad EAS AF: 0.000278

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0218

Gnomad MID AF: 0.0636

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0285

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

GnomAD4 genome AF: 0.0229 AC: 2563 AN: 111997 Hom.: 33 Cov.: 23 AF XY: 0.0225 AC XY: 770 AN XY: 34161

Gnomad4 AFR AF: 0.00479

Gnomad4 AMR AF: 0.0201

Gnomad4 ASJ AF: 0.00945

Gnomad4 EAS AF: 0.000279

Gnomad4 SAS AF: 0.0179

Gnomad4 FIN AF: 0.0218

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.0282

Alfa AF: 0.0335 Hom.: 905

Bravo AF: 0.0224

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3131301; hg19: chrX-51316467;