3-88475025-C-T

Variant names:

• chr3-88475025-C-T
• rs2880961

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 0.295 in 151,962 control chromosomes in the GnomAD database, including 7,331 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 0.30 (7331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 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: 0.295 AC: 44860 AN: 151846 Hom.: 7319 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.295 AC: 44896 AN: 151962 Hom.: 7331 Cov.: 32 AF XY: 0.305 AC XY: 22654 AN XY: 74256

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.317

Alfa AF: 0.305 Hom.: 17147

Bravo AF: 0.301

Asia WGS AF: 0.367 AC: 1272 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2880961; hg19: chr3-88524175;