20-1225242-T-C

Variant names:

• chr20-1225242-T-C
• rs397020

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 0.577 in 152,118 control chromosomes in the GnomAD database, including 26,932 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 0.58 (26932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 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: 0.577 AC: 87651 AN: 152000 Hom.: 26889 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.577 AC: 87755 AN: 152118 Hom.: 26932 Cov.: 32 AF XY: 0.569 AC XY: 42339 AN XY: 74372

African (AFR) AF: 0.792 AC: 32856 AN: 41492

American (AMR) AF: 0.507 AC: 7749 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1507 AN: 5184

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4826

European-Finnish (FIN) AF: 0.470 AC: 4972 AN: 10572

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35552 AN: 67980

Other (OTH) AF: 0.556 AC: 1174 AN: 2110

Alfa AF: 0.531 Hom.: 54814

Bravo AF: 0.590

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs397020; hg19: chr20-1205886;