12-89912002-A-G

Variant names:

• chr12-89912002-A-G
• rs7965584
• ENST00000547370.5:n.228-9065A>G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000547370.5(ENSG00000258216):​n.228-9065A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0041 (3 hom., cov: 18)
• Consequence: ENSG00000258216 ENST00000547370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

ENSG00000258216 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 3 gene

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
ENSG00000258216	ENST00000547370.5	n.228-9065A>G		intron_variant	Intron 1 of 3	4
ENSG00000258216	ENST00000651272.1	n.402-9065A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.00406 AC: 480 AN: 118212 Hom.: 3 Cov.: 18

Gnomad AFR AF: 0.00151

Gnomad AMI AF: 0.00159

Gnomad AMR AF: 0.00297

Gnomad ASJ AF: 0.00110

Gnomad EAS AF: 0.0107

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.000587

Gnomad MID AF: 0.0115

Gnomad NFE AF: 0.00569

Gnomad OTH AF: 0.00743

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

GnomAD4 genome AF: 0.00406 AC: 480 AN: 118304 Hom.: 3 Cov.: 18 AF XY: 0.00435 AC XY: 249 AN XY: 57260

Gnomad4 AFR AF: 0.00150

Gnomad4 AMR AF: 0.00296

Gnomad4 ASJ AF: 0.00110

Gnomad4 EAS AF: 0.0107

Gnomad4 SAS AF: 0.0107

Gnomad4 FIN AF: 0.000587

Gnomad4 NFE AF: 0.00569

Gnomad4 OTH AF: 0.00737

Alfa AF: 0.0932 Hom.: 26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7965584; hg19: chr12-90305779;