rs12330441

Variant names:

• chr3-137086757-T-G
• rs12330441

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 0.0589 in 152,236 control chromosomes in the GnomAD database, including 304 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 0.059 (304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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: 0.0590 AC: 8969 AN: 152118 Hom.: 303 Cov.: 32

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0589 AC: 8974 AN: 152236 Hom.: 304 Cov.: 32 AF XY: 0.0595 AC XY: 4428 AN XY: 74436

Gnomad4 AFR AF: 0.0418

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0350

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.0673

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0610 Hom.: 408

Bravo AF: 0.0560

Asia WGS AF: 0.108 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12330441; hg19: chr3-136805599;