1-118483467-C-T

Variant names:

• chr1-118483467-C-T
• rs1146313

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 0.604 in 151,956 control chromosomes in the GnomAD database, including 29,616 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 0.60 (29616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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: 0.604 AC: 91686 AN: 151838 Hom.: 29543 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.604 AC: 91822 AN: 151956 Hom.: 29616 Cov.: 32 AF XY: 0.608 AC XY: 45187 AN XY: 74268

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.556

Alfa AF: 0.489 Hom.: 23987

Bravo AF: 0.621

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1146313; hg19: chr1-119026090;