chr3-184148012-T-A

Position:

• chr3-184148012-T-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 0.467 in 151,820 control chromosomes in the GnomAD database, including 16,788 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 0.47 (16788 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 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: 0.467 AC: 70864 AN: 151702 Hom.: 16770 Cov.: 31

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.467 AC: 70921 AN: 151820 Hom.: 16788 Cov.: 31 AF XY: 0.468 AC XY: 34733 AN XY: 74174

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.455

Alfa AF: 0.280 Hom.: 620

Bravo AF: 0.462

Asia WGS AF: 0.564 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs843360; hg19: chr3-183865800;