rs4453857

Positions:

• chr3-162027101-G-C

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 0.0204 in 151,774 control chromosomes in the GnomAD database, including 157 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 0.020 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 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: 0.0205 AC: 3107 AN: 151656 Hom.: 159 Cov.: 32

Gnomad AFR AF: 0.00462

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0282

Gnomad ASJ AF: 0.0191

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0204 AC: 3096 AN: 151774 Hom.: 157 Cov.: 32 AF XY: 0.0243 AC XY: 1801 AN XY: 74164

Gnomad4 AFR AF: 0.00461

Gnomad4 AMR AF: 0.0283

Gnomad4 ASJ AF: 0.0191

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.000754

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0129 Hom.: 10

Bravo AF: 0.0190

Asia WGS AF: 0.124 AC: 433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4453857; hg19: chr3-161744889;