chr1-153461216-T-C

Variant names:

• chr1-153461216-T-C
• rs3006433

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 0.864 in 152,278 control chromosomes in the GnomAD database, including 57,196 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 0.86 (57196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 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: 0.864 AC: 131449 AN: 152160 Hom.: 57123 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.864 AC: 131583 AN: 152278 Hom.: 57196 Cov.: 32 AF XY: 0.863 AC XY: 64248 AN XY: 74456

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.848

Alfa AF: 0.863 Hom.: 7070

Bravo AF: 0.864

Asia WGS AF: 0.751 AC: 2614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3006433; hg19: chr1-153433692;