rs1229078

Positions:

• chrX-16203781-T-A

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 0.398 in 110,660 control chromosomes in the GnomAD database, including 6,987 homozygotes. There are 12,334 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 0.40 (6987 hom., 12334 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.16203781T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.398 AC: 43977 AN: 110610 Hom.: 6988 Cov.: 22 AF XY: 0.374 AC XY: 12304 AN XY: 32894

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.398 AC: 44002 AN: 110660 Hom.: 6987 Cov.: 22 AF XY: 0.374 AC XY: 12334 AN XY: 32954

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.369

Alfa AF: 0.374 Hom.: 2488

Bravo AF: 0.417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1229078; hg19: chrX-16221904;