3-88483065-G-A

Position:

• chr3-88483065-G-A

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 0.262 in 151,638 control chromosomes in the GnomAD database, including 5,834 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 0.26 (5834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39657 AN: 151520 Hom.: 5816 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.262 AC: 39705 AN: 151638 Hom.: 5834 Cov.: 32 AF XY: 0.270 AC XY: 20027 AN XY: 74048

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.279

Alfa AF: 0.267 Hom.: 2658

Bravo AF: 0.266

Asia WGS AF: 0.308 AC: 1067 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
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: rs2344953; hg19: chr3-88532215;