rs1399272

Variant names:

• chr3-102092932-T-C
• rs1399272

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 0.369 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

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 (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.396

Alfa AF: 0.403 Hom.: 7083

Bravo AF: 0.366

Asia WGS AF: 0.624 AC: 2171 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	1.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1399272; hg19: chr3-101811776;