rs2296236

Variant names:

• chr20-3039444-C-T
• rs2296236

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 0.173 in 152,242 control chromosomes in the GnomAD database, including 2,554 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 0.17 (2554 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 0.173 AC: 26352 AN: 152124 Hom.: 2538 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.173 AC: 26399 AN: 152242 Hom.: 2554 Cov.: 33 AF XY: 0.179 AC XY: 13316 AN XY: 74436

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.170

Alfa AF: 0.169 Hom.: 3076

Bravo AF: 0.172

Asia WGS AF: 0.329 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2296236; hg19: chr20-3020090;