rs7595886

Variant names:

• chr2-191174012-C-T
• rs7595886
• ENST00000431429.1:n.-221C>T

Variant summary

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

The ENST00000431429.1(HMGB1P27):​n.-221C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,106 control chromosomes in the GnomAD database, including 7,348 homozygotes. 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 0.25 (7348 hom., cov: 32)
• Consequence: HMGB1P27 ENST00000431429.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

HMGB1P27 (HGNC:39118): (high mobility group box 1 pseudogene 27)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 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
HMGB1P27	ENST00000431429.1	n.-221C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37491 AN: 151988 Hom.: 7319 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0643

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.247 AC: 37577 AN: 152106 Hom.: 7348 Cov.: 32 AF XY: 0.239 AC XY: 17793 AN XY: 74358

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0643

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.233

Alfa AF: 0.148 Hom.: 3706

Bravo AF: 0.268

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7595886; hg19: chr2-192038738;