20-6686488-A-T

Variant names:

• chr20-6686488-A-T
• rs2223753

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 0.371 in 151,960 control chromosomes in the GnomAD database, including 12,363 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 0.37 (12363 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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: 0.371 AC: 56353 AN: 151842 Hom.: 12370 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.371 AC: 56342 AN: 151960 Hom.: 12363 Cov.: 31 AF XY: 0.364 AC XY: 27011 AN XY: 74268

African (AFR) AF: 0.138 AC: 5744 AN: 41490

American (AMR) AF: 0.406 AC: 6199 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1407 AN: 5166

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4814

European-Finnish (FIN) AF: 0.459 AC: 4833 AN: 10522

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33785 AN: 67932

Other (OTH) AF: 0.381 AC: 805 AN: 2112

Alfa AF: 0.439 Hom.: 1965

Bravo AF: 0.364

Asia WGS AF: 0.248 AC: 860 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	8.0
DANN	Benign	0.79
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2223753; hg19: chr20-6667135;