3-188077537-G-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 0.28 in 152,016 control chromosomes in the GnomAD database, including 6,567 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 0.28 (6567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 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: 0.280 AC: 42600 AN: 151898 Hom.: 6563 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.280 AC: 42627 AN: 152016 Hom.: 6567 Cov.: 32 AF XY: 0.275 AC XY: 20454 AN XY: 74332

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.0717

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.289

Alfa AF: 0.232 Hom.: 1476

Bravo AF: 0.285

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.67
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9871228; hg19: chr3-187795325;