1-186683820-G-T

Variant names:

• chr1-186683820-G-T
• rs2383515

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 0.218 in 151,942 control chromosomes in the GnomAD database, including 4,663 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 0.22 (4663 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33095 AN: 151824 Hom.: 4643 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.218 AC: 33154 AN: 151942 Hom.: 4663 Cov.: 32 AF XY: 0.213 AC XY: 15791 AN XY: 74248

African (AFR) AF: 0.391 AC: 16165 AN: 41370

American (AMR) AF: 0.187 AC: 2852 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.0484 AC: 250 AN: 5168

South Asian (SAS) AF: 0.165 AC: 793 AN: 4820

European-Finnish (FIN) AF: 0.0871 AC: 920 AN: 10564

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10750 AN: 67966

Other (OTH) AF: 0.223 AC: 471 AN: 2112

Alfa AF: 0.218 Hom.: 641

Bravo AF: 0.234

Asia WGS AF: 0.159 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.45
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2383515; hg19: chr1-186652952;