rs1146161

Variant names:

• chr1-115116155-A-C
• rs1146161

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 0.824 in 152,032 control chromosomes in the GnomAD database, including 51,651 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 0.82 (51651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.824 AC: 125143 AN: 151916 Hom.: 51607 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.824 AC: 125244 AN: 152032 Hom.: 51651 Cov.: 31 AF XY: 0.822 AC XY: 61013 AN XY: 74270

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.806

Alfa AF: 0.828 Hom.: 28193

Bravo AF: 0.830

Asia WGS AF: 0.864 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1146161; hg19: chr1-115658776;