20-680009-A-T

Variant names:

• chr20-680009-A-T
• rs7272428

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 0.281 in 152,136 control chromosomes in the GnomAD database, including 6,656 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 0.28 (6656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.281 AC: 42680 AN: 152018 Hom.: 6640 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.281 AC: 42740 AN: 152136 Hom.: 6656 Cov.: 33 AF XY: 0.273 AC XY: 20292 AN XY: 74382

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.268

Alfa AF: 0.159 Hom.: 300

Bravo AF: 0.287

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7272428; hg19: chr20-660653;