rs2820446

Variant names:

• chr1-219575476-C-G
• rs2820446

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0751 AC: 3119 AN: 41558

American (AMR) AF: 0.398 AC: 6088 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3468

East Asian (EAS) AF: 0.263 AC: 1367 AN: 5188

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4830

European-Finnish (FIN) AF: 0.281 AC: 2970 AN: 10588

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19086 AN: 67992

Other (OTH) AF: 0.269 AC: 569 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.50
PhyloP100		0.34

Splicing

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

Other links and lift over

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