rs1036360

Variant names:

• chr12-94059553-A-G
• rs1036360
• ENST00000786512.1:n.124+11591A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000786512.1(ENSG00000302422):​n.124+11591A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000302422 ENST00000786512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 1 publications found

Genes affected

ENSG00000302422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786512.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302422	ENST00000786512.1		n.124+11591A>G		intron	N/A

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

African (AFR) AF: 0.339 AC: 14050 AN: 41482

American (AMR) AF: 0.397 AC: 6071 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3464

East Asian (EAS) AF: 0.527 AC: 2730 AN: 5176

South Asian (SAS) AF: 0.509 AC: 2451 AN: 4814

European-Finnish (FIN) AF: 0.202 AC: 2135 AN: 10588

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20695 AN: 67958

Other (OTH) AF: 0.361 AC: 763 AN: 2116

Alfa AF: 0.323 Hom.: 8664

Bravo AF: 0.341

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs1036360; hg19: chr12-94453329;