chr3-12435556-G-C

Variant names:

• chr3-12435556-G-C
• rs1152003

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 0.561 in 151,956 control chromosomes in the GnomAD database, including 25,275 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 0.56 (25275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 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: 0.561 AC: 85156 AN: 151838 Hom.: 25266 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.561 AC: 85190 AN: 151956 Hom.: 25275 Cov.: 32 AF XY: 0.560 AC XY: 41608 AN XY: 74274

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.560

Alfa AF: 0.607 Hom.: 3596

Bravo AF: 0.536

Asia WGS AF: 0.503 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1152003; hg19: chr3-12477055;