rs10241628

Variant names:

• chr7-55877867-A-G
• rs10241628
• ENST00000452998.1:n.-45A>G

Variant summary

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

The ENST00000452998.1(ENSG00000227499):​n.-45A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 672,468 control chromosomes in the GnomAD database, including 1,654 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 0.077 (1180 hom., cov: 33)
  • Exomes 𝑓: 0.021 (474 hom.)
• Consequence: ENSG00000227499 ENST00000452998.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

ENSG00000227499 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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
ENSG00000227499	ENST00000452998.1	n.-45A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11682 AN: 152154 Hom.: 1175 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00631

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0183

Gnomad OTH AF: 0.0659

GnomAD4 exome AF: 0.0210 AC: 10902 AN: 520196 Hom.: 474 Cov.: 5 AF XY: 0.0193 AC XY: 5411 AN XY: 280472

Gnomad4 AFR exome AF: 0.227

Gnomad4 AMR exome AF: 0.0262

Gnomad4 ASJ exome AF: 0.0157

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00233

Gnomad4 FIN exome AF: 0.00731

Gnomad4 NFE exome AF: 0.0178

Gnomad4 OTH exome AF: 0.0286

GnomAD4 genome AF: 0.0768 AC: 11702 AN: 152272 Hom.: 1180 Cov.: 33 AF XY: 0.0740 AC XY: 5509 AN XY: 74450

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0150

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00311

Gnomad4 FIN AF: 0.00631

Gnomad4 NFE AF: 0.0183

Gnomad4 OTH AF: 0.0652

Alfa AF: 0.0509 Hom.: 88

Bravo AF: 0.0855

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10241628; hg19: chr7-55945560;