chr1-190021282-G-A

Variant names:

• chr1-190021282-G-A
• rs4845214

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 0.673 in 152,042 control chromosomes in the GnomAD database, including 34,744 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 0.67 (34744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 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: 0.673 AC: 102227 AN: 151922 Hom.: 34678 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.673 AC: 102360 AN: 152042 Hom.: 34744 Cov.: 32 AF XY: 0.674 AC XY: 50075 AN XY: 74324

African (AFR) AF: 0.759 AC: 31474 AN: 41466

American (AMR) AF: 0.634 AC: 9678 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2291 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2595 AN: 5152

South Asian (SAS) AF: 0.660 AC: 3184 AN: 4822

European-Finnish (FIN) AF: 0.709 AC: 7494 AN: 10570

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43396 AN: 67998

Other (OTH) AF: 0.660 AC: 1391 AN: 2108

Alfa AF: 0.656 Hom.: 4063

Bravo AF: 0.669

Asia WGS AF: 0.626 AC: 2177 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	2.8
DANN	Benign	0.68
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4845214; hg19: chr1-189990412;