rs2820443

chr1-219580167-T-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 0.232 in 152,126 control chromosomes in the GnomAD database, including 4,992 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 (4992 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35318 AN: 152008 Hom.: 4986 Cov.: 30

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.232 AC: 35333 AN: 152126 Hom.: 4992 Cov.: 30 AF XY: 0.236 AC XY: 17532 AN XY: 74344

Gnomad4 AFR AF: 0.0748

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.268

Alfa AF: 0.260 Hom.: 1466

Bravo AF: 0.239

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	16
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2820443; hg19: chr1-219753509; COSMIC: COSV60029500;