rs2021899

Positions:

• chr6-170596889-G-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;