rs2157056

chr3-46324292-G-A

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 0.217 in 152,072 control chromosomes in the GnomAD database, including 4,396 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 0.22 (4396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 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: 0.218 AC: 33061 AN: 151954 Hom.: 4397 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0916

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.217 AC: 33049 AN: 152072 Hom.: 4396 Cov.: 32 AF XY: 0.216 AC XY: 16066 AN XY: 74336

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0917

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.218

Alfa AF: 0.242 Hom.: 755

Bravo AF: 0.204

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.3
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2157056; hg19: chr3-46365783;