chr3-102092932-T-C

Variant names:

• chr3-102092932-T-C
• rs1399272

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 0.369 in 152,102 control chromosomes in the GnomAD database, including 12,276 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 0.37 (12276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.369 AC: 56095 AN: 151984 Hom.: 12266 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.369 AC: 56125 AN: 152102 Hom.: 12276 Cov.: 32 AF XY: 0.379 AC XY: 28163 AN XY: 74380

African (AFR) AF: 0.162 AC: 6719 AN: 41486

American (AMR) AF: 0.464 AC: 7080 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1559 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4445 AN: 5192

South Asian (SAS) AF: 0.539 AC: 2601 AN: 4828

European-Finnish (FIN) AF: 0.433 AC: 4585 AN: 10588

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27682 AN: 67958

Other (OTH) AF: 0.396 AC: 834 AN: 2106

Alfa AF: 0.401 Hom.: 7916

Bravo AF: 0.366

Asia WGS AF: 0.624 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1399272; hg19: chr3-101811776;