rs12330727

Variant names:

• chr3-101114904-T-C
• rs12330727

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 0.192 in 152,088 control chromosomes in the GnomAD database, including 4,106 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 0.19 (4106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.192 AC: 29123 AN: 151970 Hom.: 4087 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0620

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.192 AC: 29174 AN: 152088 Hom.: 4106 Cov.: 32 AF XY: 0.185 AC XY: 13727 AN XY: 74392

African (AFR) AF: 0.401 AC: 16606 AN: 41452

American (AMR) AF: 0.105 AC: 1604 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0568 AC: 197 AN: 3468

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5186

South Asian (SAS) AF: 0.0625 AC: 302 AN: 4832

European-Finnish (FIN) AF: 0.0960 AC: 1018 AN: 10600

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9038 AN: 67968

Other (OTH) AF: 0.163 AC: 344 AN: 2110

Alfa AF: 0.144 Hom.: 1052

Bravo AF: 0.201

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.53
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12330727; hg19: chr3-100833748;