rs1482853

Positions:

• chr3-157080684-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.363 in 152,052 control chromosomes in the GnomAD database, including 10,521 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 0.36 (10521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55187 AN: 151934 Hom.: 10526 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.363 AC: 55202 AN: 152052 Hom.: 10521 Cov.: 32 AF XY: 0.359 AC XY: 26668 AN XY: 74342

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.407

Alfa AF: 0.385 Hom.: 1456

Bravo AF: 0.371

Asia WGS AF: 0.355 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	13
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1482853; hg19: chr3-156798473;