rs369270

Variant names:

• chr20-5048561-A-G
• rs369270

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 0.414 in 152,072 control chromosomes in the GnomAD database, including 13,669 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 0.41 (13669 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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: 0.415 AC: 62986 AN: 151954 Hom.: 13667 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.414 AC: 63000 AN: 152072 Hom.: 13669 Cov.: 33 AF XY: 0.420 AC XY: 31182 AN XY: 74320

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.400

Alfa AF: 0.422 Hom.: 26558

Bravo AF: 0.409

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs369270; hg19: chr20-5029207;