chr3-153273601-A-T

Position:

• chr3-153273601-A-T

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 0.0384 in 152,302 control chromosomes in the GnomAD database, including 154 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 0.038 (154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918

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 (NFE) allele frequency at 95% confidence interval = 0.0589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5841 AN: 152184 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.00636

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.00895

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0384 AC: 5841 AN: 152302 Hom.: 154 Cov.: 32 AF XY: 0.0362 AC XY: 2697 AN XY: 74480

Gnomad4 AFR AF: 0.0114

Gnomad4 AMR AF: 0.0365

Gnomad4 ASJ AF: 0.0645

Gnomad4 EAS AF: 0.00638

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.00895

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0455 Hom.: 19

Bravo AF: 0.0388

Asia WGS AF: 0.0200 AC: 70 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	0.68
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513442; hg19: chr3-152991390;