3-102055199-G-C

Variant names:

• chr3-102055199-G-C
• rs991258

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 0.286 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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.286 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

African (AFR) AF: 0.218 AC: 9019 AN: 41454

American (AMR) AF: 0.351 AC: 5368 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3136 AN: 5150

South Asian (SAS) AF: 0.350 AC: 1683 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4067 AN: 10536

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18507 AN: 67974

Other (OTH) AF: 0.256 AC: 539 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs991258; hg19: chr3-101774043; COSMIC: COSV107175774;