rs1485405

Variant names:

• chr12-30129954-A-G
• rs1485405
• ENST00000653361.1:n.279-373A>G

Variant summary

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

The ENST00000653361.1(ENSG00000286566):​n.279-373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,054 control chromosomes in the GnomAD database, including 13,647 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 0.41 (13647 hom., cov: 33)
• Consequence: ENSG00000286566 ENST00000653361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 7 publications found

Genes affected

ENSG00000286566 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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
ENSG00000286566	ENST00000653361.1	n.279-373A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61806 AN: 151936 Hom.: 13631 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.407 AC: 61861 AN: 152054 Hom.: 13647 Cov.: 33 AF XY: 0.405 AC XY: 30141 AN XY: 74336

African (AFR) AF: 0.233 AC: 9649 AN: 41494

American (AMR) AF: 0.429 AC: 6555 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3468

East Asian (EAS) AF: 0.244 AC: 1261 AN: 5166

South Asian (SAS) AF: 0.455 AC: 2190 AN: 4818

European-Finnish (FIN) AF: 0.501 AC: 5285 AN: 10546

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33794 AN: 67968

Other (OTH) AF: 0.406 AC: 856 AN: 2108

Alfa AF: 0.461 Hom.: 24211

Bravo AF: 0.395

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.21
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1485405; hg19: chr12-30282887;