rs2021899

Variant names:

• chr6-170596889-G-C
• rs2021899

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 0.579 in 152,008 control chromosomes in the GnomAD database, including 26,555 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 0.58 (26555 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.77 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: 0.579 AC: 87945 AN: 151890 Hom.: 26503 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.579 AC: 88048 AN: 152008 Hom.: 26555 Cov.: 31 AF XY: 0.576 AC XY: 42771 AN XY: 74308

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.564

Alfa AF: 0.548 Hom.: 2932

Bravo AF: 0.593

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2021899; hg19: chr6-170905977;