rs2157056

Variant names:

• chr3-46324292-G-A
• rs2157056

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0797 AC: 3308 AN: 41488

American (AMR) AF: 0.214 AC: 3276 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3472

East Asian (EAS) AF: 0.0917 AC: 475 AN: 5182

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3185 AN: 10550

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20319 AN: 67952

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.236 Hom.: 758

Bravo AF: 0.204

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2157056; hg19: chr3-46365783;