1-115594189-C-T

Variant names:

• chr1-115594189-C-T
• rs3860222

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 0.585 in 151,868 control chromosomes in the GnomAD database, including 31,262 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 0.59 (31262 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.585 AC: 88845 AN: 151750 Hom.: 31264 Cov.: 30

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.585 AC: 88849 AN: 151868 Hom.: 31262 Cov.: 30 AF XY: 0.581 AC XY: 43087 AN XY: 74188

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.625

Alfa AF: 0.749 Hom.: 54987

Bravo AF: 0.571

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3860222; hg19: chr1-116136810;