rs1478290

Variant names:

• chr12-21608381-A-C
• rs1478290
• ENST00000647960.1:n.*123+22280T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-21608381-A-C
• chr12-21608381-A-G
• chr12-21608381-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647960.1(ENSG00000285854):​n.*123+22280T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,064 control chromosomes in the GnomAD database, including 6,580 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 0.28 (6580 hom., cov: 31)
• Consequence: ENSG00000285854 ENST00000647960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519

Genes affected

ENSG00000285854 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 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
ENSG00000285854	ENST00000647960.1	n.*123+22280T>G		intron_variant	Intron 8 of 22			ENSP00000497202.1
ENSG00000285854	ENST00000648372.1	n.106+27158T>G		intron_variant	Intron 1 of 10

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42763 AN: 151946 Hom.: 6578 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.281 AC: 42791 AN: 152064 Hom.: 6580 Cov.: 31 AF XY: 0.288 AC XY: 21391 AN XY: 74324

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.280

Alfa AF: 0.299 Hom.: 11465

Bravo AF: 0.267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478290; hg19: chr12-21761315;