rs7252525

Variant names:

• chr19-54298005-C-T
• rs7252525
• ENST00000514037.1:n.*100G>A

Variant summary

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

The ENST00000514037.1(ENSG00000251431):​n.*100G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0674 in 152,486 control chromosomes in the GnomAD database, including 395 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 0.067 (394 hom., cov: 32)
  • Exomes 𝑓: 0.048 (1 hom.)
• Consequence: ENSG00000251431 ENST00000514037.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694

Genes affected

ENSG00000251431 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 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
ENSG00000251431	ENST00000514037.1	n.*100G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0675 AC: 10267 AN: 152158 Hom.: 393 Cov.: 32

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0762

GnomAD4 exome AF: 0.0476 AC: 10 AN: 210 Hom.: 1 Cov.: 0 AF XY: 0.0714 AC XY: 8 AN XY: 112

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.125

Gnomad4 FIN exome AF: 0.0294

Gnomad4 NFE exome AF: 0.0446

Gnomad4 OTH exome AF: 0.0750

GnomAD4 genome AF: 0.0674 AC: 10263 AN: 152276 Hom.: 394 Cov.: 32 AF XY: 0.0675 AC XY: 5024 AN XY: 74454

Gnomad4 AFR AF: 0.0347

Gnomad4 AMR AF: 0.0573

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.0858

Gnomad4 NFE AF: 0.0881

Gnomad4 OTH AF: 0.0750

Alfa AF: 0.0853 Hom.: 621

Bravo AF: 0.0635

Asia WGS AF: 0.0400 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7252525; hg19: chr19-54808614;