rs1036360

Positions:

• chr12-94059553-A-G

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 0.331 in 152,090 control chromosomes in the GnomAD database, including 8,681 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 0.33 (8681 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50281 AN: 151972 Hom.: 8671 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.331 AC: 50331 AN: 152090 Hom.: 8681 Cov.: 33 AF XY: 0.334 AC XY: 24814 AN XY: 74354

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.361

Alfa AF: 0.320 Hom.: 6655

Bravo AF: 0.341

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1036360; hg19: chr12-94453329;