1-121470889-C-T

Variant names:

• chr1-121470889-C-T
• rs12033387

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 0.0381 in 152,242 control chromosomes in the GnomAD database, including 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 0.038 (262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 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: 0.0381 AC: 5797 AN: 152124 Hom.: 260 Cov.: 32

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0885

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.00781

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0381 AC: 5800 AN: 152242 Hom.: 262 Cov.: 32 AF XY: 0.0403 AC XY: 2998 AN XY: 74432

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.0373

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0877

Gnomad4 FIN AF: 0.0158

Gnomad4 NFE AF: 0.00781

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0130 Hom.: 18

Bravo AF: 0.0395

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12033387; hg19: chr1-121212743;