rs1482853

Variant names:

• chr3-157080684-C-A
• rs1482853

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;