1-101500389-G-A

Variant names:

• chr1-101500389-G-A
• rs436346

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 0.795 in 151,868 control chromosomes in the GnomAD database, including 48,403 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 0.79 (48403 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120619 AN: 151750 Hom.: 48399 Cov.: 29

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.795 AC: 120661 AN: 151868 Hom.: 48403 Cov.: 29 AF XY: 0.793 AC XY: 58841 AN XY: 74208

African (AFR) AF: 0.738 AC: 30538 AN: 41400

American (AMR) AF: 0.659 AC: 10048 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3032 AN: 3466

East Asian (EAS) AF: 0.870 AC: 4463 AN: 5128

South Asian (SAS) AF: 0.731 AC: 3521 AN: 4814

European-Finnish (FIN) AF: 0.835 AC: 8804 AN: 10550

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57436 AN: 67952

Other (OTH) AF: 0.827 AC: 1744 AN: 2108

Alfa AF: 0.817 Hom.: 16325

Bravo AF: 0.776

Asia WGS AF: 0.779 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.73
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs436346; hg19: chr1-101965945;