1-153461216-T-C

Variant names:

• chr1-153461216-T-C
• rs3006433

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.945 AC: 39253 AN: 41550

American (AMR) AF: 0.842 AC: 12881 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3470

East Asian (EAS) AF: 0.742 AC: 3842 AN: 5176

South Asian (SAS) AF: 0.702 AC: 3387 AN: 4826

European-Finnish (FIN) AF: 0.911 AC: 9666 AN: 10612

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56884 AN: 68020

Other (OTH) AF: 0.848 AC: 1793 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.36
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3006433; hg19: chr1-153433692;