chr3-109918921-G-A

Variant names:

• chr3-109918921-G-A
• rs56100358

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 0.293 in 151,980 control chromosomes in the GnomAD database, including 6,685 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 (6685 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44484 AN: 151862 Hom.: 6675 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.293 AC: 44519 AN: 151980 Hom.: 6685 Cov.: 31 AF XY: 0.297 AC XY: 22038 AN XY: 74258

African (AFR) AF: 0.232 AC: 9639 AN: 41476

American (AMR) AF: 0.246 AC: 3760 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1558 AN: 5136

South Asian (SAS) AF: 0.440 AC: 2118 AN: 4814

European-Finnish (FIN) AF: 0.311 AC: 3275 AN: 10546

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22011 AN: 67970

Other (OTH) AF: 0.307 AC: 645 AN: 2104

Alfa AF: 0.197 Hom.: 469

Bravo AF: 0.281

Asia WGS AF: 0.354 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs56100358; hg19: chr3-109637768;