20-6632185-A-G

Variant names:

• chr20-6632185-A-G
• rs1884897

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 0.626 in 151,964 control chromosomes in the GnomAD database, including 30,222 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 0.63 (30222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.626 AC: 94993 AN: 151846 Hom.: 30193 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.626 AC: 95071 AN: 151964 Hom.: 30222 Cov.: 32 AF XY: 0.629 AC XY: 46732 AN XY: 74262

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.624

Alfa AF: 0.635 Hom.: 63028

Bravo AF: 0.628

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1884897; hg19: chr20-6612832;