rs1321450

Variant names:

• chr20-6596257-C-T
• rs1321450

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 0.255 in 152,124 control chromosomes in the GnomAD database, including 5,283 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 0.26 (5283 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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: 0.255 AC: 38774 AN: 152006 Hom.: 5271 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0953

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.255 AC: 38817 AN: 152124 Hom.: 5283 Cov.: 33 AF XY: 0.252 AC XY: 18734 AN XY: 74358

African (AFR) AF: 0.332 AC: 13786 AN: 41504

American (AMR) AF: 0.255 AC: 3892 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.0954 AC: 493 AN: 5170

South Asian (SAS) AF: 0.185 AC: 890 AN: 4822

European-Finnish (FIN) AF: 0.232 AC: 2447 AN: 10570

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15695 AN: 67992

Other (OTH) AF: 0.241 AC: 508 AN: 2106

Alfa AF: 0.244 Hom.: 584

Bravo AF: 0.262

Asia WGS AF: 0.134 AC: 465 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.76
DANN	Benign	0.47
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1321450; hg19: chr20-6576904;