3-152990140-T-C

Variant names:

• chr3-152990140-T-C
• rs2056527

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 0.788 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.788 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

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.849

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.751

Alfa AF: 0.705 Hom.: 2408

Bravo AF: 0.791

Asia WGS AF: 0.769 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056527; hg19: chr3-152707929;