chr3-102055199-G-C

Position:

• chr3-102055199-G-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 0.286 in 151,978 control chromosomes in the GnomAD database, including 6,857 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 0.29 (6857 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 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: 0.286 AC: 43386 AN: 151860 Hom.: 6864 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.286 AC: 43402 AN: 151978 Hom.: 6857 Cov.: 32 AF XY: 0.295 AC XY: 21929 AN XY: 74268

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.256

Alfa AF: 0.264 Hom.: 3167

Bravo AF: 0.283

Asia WGS AF: 0.452 AC: 1571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs991258; hg19: chr3-101774043;