rs7252525

Positions:

• chr19-54298005-C-T

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 0.0674 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.694

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/exons	MANE	Protein	UniProt

Ensembl

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

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;