3-110208529-A-G

Variant names:

• chr3-110208529-A-G
• rs13323983

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 0.154 in 152,044 control chromosomes in the GnomAD database, including 2,133 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 0.15 (2133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.154 AC: 23376 AN: 151926 Hom.: 2133 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.00752

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.154 AC: 23371 AN: 152044 Hom.: 2133 Cov.: 32 AF XY: 0.152 AC XY: 11290 AN XY: 74308

African (AFR) AF: 0.0826 AC: 3428 AN: 41500

American (AMR) AF: 0.132 AC: 2015 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 807 AN: 3470

East Asian (EAS) AF: 0.00754 AC: 39 AN: 5172

South Asian (SAS) AF: 0.0677 AC: 327 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2240 AN: 10584

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13848 AN: 67910

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.186 Hom.: 5004

Bravo AF: 0.147

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs13323983; hg19: chr3-109927376;