12-7182621-T-C

Variant names:

• chr12-7182621-T-C
• rs12828421
• ENST00000543061.1:n.324+6125A>G

Variant summary

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

The ENST00000543061.1(ENSG00000255572):​n.324+6125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,000 control chromosomes in the GnomAD database, including 16,274 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 0.44 (16274 hom., cov: 31)
• Consequence: ENSG00000255572 ENST00000543061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 11 publications found

Genes affected

ENSG00000255572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 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
ENSG00000255572	ENST00000543061.1	n.324+6125A>G		intron_variant	Intron 1 of 1	2
ENSG00000255572	ENST00000545794.1	n.279+6125A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67163 AN: 151886 Hom.: 16265 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.442 AC: 67191 AN: 152000 Hom.: 16274 Cov.: 31 AF XY: 0.441 AC XY: 32722 AN XY: 74280

African (AFR) AF: 0.246 AC: 10187 AN: 41456

American (AMR) AF: 0.607 AC: 9273 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1687 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1970 AN: 5162

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4651 AN: 10542

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35440 AN: 67958

Other (OTH) AF: 0.475 AC: 1002 AN: 2108

Alfa AF: 0.486 Hom.: 27732

Bravo AF: 0.447

Asia WGS AF: 0.418 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.57
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs12828421; hg19: chr12-7335217;