3-188077537-G-T

Variant names:

• chr3-188077537-G-T
• rs9871228

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.388 AC: 16075 AN: 41410

American (AMR) AF: 0.209 AC: 3190 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1383 AN: 3472

East Asian (EAS) AF: 0.0717 AC: 371 AN: 5172

South Asian (SAS) AF: 0.153 AC: 737 AN: 4816

European-Finnish (FIN) AF: 0.227 AC: 2403 AN: 10576

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17596 AN: 67974

Other (OTH) AF: 0.289 AC: 612 AN: 2114

Alfa AF: 0.243 Hom.: 2414

Bravo AF: 0.285

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.67
DANN	Benign	0.57
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs9871228; hg19: chr3-187795325;