rs187084

Positions:

• chr3-52227015-A-G
• chr3-52227015-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 0.378 in 152,132 control chromosomes in the GnomAD database, including 11,169 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 0.38 (11169 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477

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 (AMR) allele frequency at 95% confidence interval = 0.421 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: 0.378 AC: 57423 AN: 152014 Hom.: 11156 Cov.: 33

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.378 AC: 57464 AN: 152132 Hom.: 11169 Cov.: 33 AF XY: 0.379 AC XY: 28156 AN XY: 74384

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.369

Alfa AF: 0.401 Hom.: 12450

Bravo AF: 0.375

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs187084; hg19: chr3-52261031;