rs2820446

Variant names:

• chr1-219575476-C-G
• rs2820446

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 0.232 in 152,228 control chromosomes in the GnomAD database, including 4,976 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 0.23 (4976 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 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: 0.232 AC: 35249 AN: 152110 Hom.: 4971 Cov.: 35

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.232 AC: 35261 AN: 152228 Hom.: 4976 Cov.: 35 AF XY: 0.235 AC XY: 17474 AN XY: 74426

Gnomad4 AFR AF: 0.0751

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.269

Alfa AF: 0.252 Hom.: 647

Bravo AF: 0.239

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2820446; hg19: chr1-219748818; COSMIC: COSV60029481;