12-6180053-G-A

Variant names:

• chr12-6180053-G-A
• rs1558324
• ENST00000810805.1:n.109+20483C>T

Variant summary

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

The ENST00000810805.1(ENSG00000255775):​n.109+20483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,972 control chromosomes in the GnomAD database, including 19,665 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 0.49 (19665 hom., cov: 32)
• Consequence: ENSG00000255775 ENST00000810805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 23 publications found

Genes affected

ENSG00000255775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810805.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255775	ENST00000810805.1		n.109+20483C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73857 AN: 151854 Hom.: 19629 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.487 AC: 73944 AN: 151972 Hom.: 19665 Cov.: 32 AF XY: 0.479 AC XY: 35613 AN XY: 74272

African (AFR) AF: 0.722 AC: 29897 AN: 41428

American (AMR) AF: 0.335 AC: 5120 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2122 AN: 5136

South Asian (SAS) AF: 0.405 AC: 1956 AN: 4824

European-Finnish (FIN) AF: 0.372 AC: 3931 AN: 10554

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28465 AN: 67964

Other (OTH) AF: 0.425 AC: 897 AN: 2110

Alfa AF: 0.442 Hom.: 46557

Bravo AF: 0.492

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.22
DANN	Benign	0.37
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs1558324; hg19: chr12-6289219;