1-186289097-A-G

Variant names:

• chr1-186289097-A-G
• rs1293970

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 0.622 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.600

Alfa AF: 0.536 Hom.: 36081

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1293970; hg19: chr1-186258229;