20-3039444-C-T

Variant names:

• chr20-3039444-C-T
• rs2296236

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 0.173 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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.123 AC: 5123 AN: 41568

American (AMR) AF: 0.244 AC: 3733 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1895 AN: 5178

South Asian (SAS) AF: 0.301 AC: 1454 AN: 4830

European-Finnish (FIN) AF: 0.189 AC: 2002 AN: 10606

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11068 AN: 67998

Other (OTH) AF: 0.170 AC: 357 AN: 2106

Alfa AF: 0.169 Hom.: 3886

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2296236; hg19: chr20-3020090;