rs1146161

chr1-115116155-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;