chr20-4213047-G-A

Position:

• chr20-4213047-G-A

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 0.907 in 152,170 control chromosomes in the GnomAD database, including 63,418 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 0.91 (63418 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137898 AN: 152052 Hom.: 63379 Cov.: 31

Gnomad AFR AF: 0.743

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.907 AC: 137988 AN: 152170 Hom.: 63418 Cov.: 31 AF XY: 0.908 AC XY: 67568 AN XY: 74420

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.916

Alfa AF: 0.945 Hom.: 15875

Bravo AF: 0.898

Asia WGS AF: 0.954 AC: 3316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs910952; hg19: chr20-4193694;