rs3006440

Variant names:

• chr1-153323131-G-A
• rs3006440

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 0.44 in 152,066 control chromosomes in the GnomAD database, including 15,296 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 0.44 (15296 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 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: 0.440 AC: 66803 AN: 151948 Hom.: 15290 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.440 AC: 66843 AN: 152066 Hom.: 15296 Cov.: 33 AF XY: 0.435 AC XY: 32306 AN XY: 74334

African (AFR) AF: 0.364 AC: 15095 AN: 41462

American (AMR) AF: 0.388 AC: 5935 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1572 AN: 3466

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5182

South Asian (SAS) AF: 0.293 AC: 1416 AN: 4826

European-Finnish (FIN) AF: 0.522 AC: 5516 AN: 10562

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34793 AN: 67972

Other (OTH) AF: 0.436 AC: 921 AN: 2114

Alfa AF: 0.474 Hom.: 2281

Bravo AF: 0.429

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.68
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs3006440; hg19: chr1-153295607;