X-153052595-T-C

Variant names:

• chrX-153052595-T-C
• rs6627737
• ENST00000421099.1:n.-182A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421099.1(HMGN2P48):​n.-182A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 110,343 control chromosomes in the GnomAD database, including 5,186 homozygotes. There are 10,270 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 0.33 (5186 hom., 10270 hem., cov: 22)
• Consequence: HMGN2P48 ENST00000421099.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

HMGN2P48 (HGNC:55157): (high mobility group nucleosomal binding domain 2 pseudogene 48)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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
HMGN2P48	ENST00000421099.1	n.-182A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.329 AC: 36255 AN: 110290 Hom.: 5178 Cov.: 22 AF XY: 0.314 AC XY: 10237 AN XY: 32560

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0675

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.329 AC: 36297 AN: 110343 Hom.: 5186 Cov.: 22 AF XY: 0.315 AC XY: 10270 AN XY: 32623

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.327

Alfa AF: 0.256 Hom.: 14659

Bravo AF: 0.336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6627737; hg19: chrX-152220954;