rs12330441

Variant names:

• chr3-137086757-T-G
• rs12330441

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 0.0589 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• 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

African (AFR) AF: 0.0418 AC: 1736 AN: 41546

American (AMR) AF: 0.0435 AC: 665 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0334 AC: 116 AN: 3470

East Asian (EAS) AF: 0.147 AC: 761 AN: 5160

South Asian (SAS) AF: 0.0350 AC: 169 AN: 4830

European-Finnish (FIN) AF: 0.0698 AC: 741 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0673 AC: 4577 AN: 68010

Other (OTH) AF: 0.0554 AC: 117 AN: 2112

Alfa AF: 0.0605 Hom.: 517

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs12330441; hg19: chr3-136805599;