1-186289097-A-G

Variant names:

• chr1-186289097-A-G
• rs1293970

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 0.622 in 151,794 control chromosomes in the GnomAD database, including 30,594 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 0.62 (30594 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.334
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94375 AN: 151676 Hom.: 30569 Cov.: 30

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.622 AC: 94443 AN: 151794 Hom.: 30594 Cov.: 30 AF XY: 0.630 AC XY: 46719 AN XY: 74182

African (AFR) AF: 0.761 AC: 31495 AN: 41380

American (AMR) AF: 0.556 AC: 8477 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1861 AN: 3460

East Asian (EAS) AF: 0.946 AC: 4874 AN: 5154

South Asian (SAS) AF: 0.743 AC: 3562 AN: 4792

European-Finnish (FIN) AF: 0.596 AC: 6263 AN: 10514

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35931 AN: 67936

Other (OTH) AF: 0.600 AC: 1261 AN: 2102

Alfa AF: 0.554 Hom.: 91345

Bravo AF: 0.625

Asia WGS AF: 0.769 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1293970; hg19: chr1-186258229;