chr3-102092932-T-C

Position:

• chr3-102092932-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;