rs4830487

Positions:

• chrX-13112365-T-C

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 0.34 in 110,606 control chromosomes in the GnomAD database, including 5,333 homozygotes. There are 11,460 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 (5333 hom., 11460 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13112365T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.340 AC: 37585 AN: 110552 Hom.: 5328 Cov.: 22 AF XY: 0.349 AC XY: 11446 AN XY: 32774

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.340 AC: 37597 AN: 110606 Hom.: 5333 Cov.: 22 AF XY: 0.349 AC XY: 11460 AN XY: 32838

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.319

Alfa AF: 0.392 Hom.: 36902

Bravo AF: 0.341

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.017
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4830487; hg19: chrX-13130484;