3-152990140-T-C

Variant names:

• chr3-152990140-T-C
• rs2056527

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 0.788 in 152,158 control chromosomes in the GnomAD database, including 47,878 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 0.79 (47878 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 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: 0.788 AC: 119828 AN: 152040 Hom.: 47838 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.788 AC: 119920 AN: 152158 Hom.: 47878 Cov.: 32 AF XY: 0.788 AC XY: 58611 AN XY: 74382

African (AFR) AF: 0.926 AC: 38490 AN: 41546

American (AMR) AF: 0.730 AC: 11161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4386 AN: 5166

South Asian (SAS) AF: 0.732 AC: 3523 AN: 4812

European-Finnish (FIN) AF: 0.783 AC: 8296 AN: 10598

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49456 AN: 67968

Other (OTH) AF: 0.751 AC: 1584 AN: 2110

Alfa AF: 0.754 Hom.: 66493

Bravo AF: 0.791

Asia WGS AF: 0.769 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.67
DANN	Benign	0.66
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs2056527; hg19: chr3-152707929;