12-76615280-A-G

Variant names:

• chr12-76615280-A-G
• rs2669010
• ENST00000551082.2:n.122-23A>G

Variant summary

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

The ENST00000551082.2(ENSG00000257526):​n.122-23A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,370 control chromosomes in the GnomAD database, including 21,857 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 0.53 (21837 hom., cov: 29)
  • Exomes 𝑓: 0.68 (20 hom.)
• Consequence: ENSG00000257526 ENST00000551082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 12 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551082.2. 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
	LOC105369850	NR_188081.1		n.453-23A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257526	ENST00000551082.2	TSL:3	n.122-23A>G		intron	N/A
	ENSG00000257526	ENST00000702157.2		n.496-23A>G		intron	N/A
	ENSG00000257526	ENST00000832799.1		n.419-17641A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80279 AN: 151156 Hom.: 21821 Cov.: 29

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.509

GnomAD4 exome AF: 0.677 AC: 65 AN: 96 Hom.: 20 Cov.: 0 AF XY: 0.662 AC XY: 49 AN XY: 74

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.702 AC: 59 AN: 84

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.531 AC: 80333 AN: 151274 Hom.: 21837 Cov.: 29 AF XY: 0.534 AC XY: 39426 AN XY: 73866

African (AFR) AF: 0.426 AC: 17535 AN: 41154

American (AMR) AF: 0.424 AC: 6441 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2029 AN: 3472

East Asian (EAS) AF: 0.632 AC: 3224 AN: 5102

South Asian (SAS) AF: 0.634 AC: 3030 AN: 4778

European-Finnish (FIN) AF: 0.622 AC: 6518 AN: 10480

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39835 AN: 67788

Other (OTH) AF: 0.514 AC: 1080 AN: 2100

Alfa AF: 0.564 Hom.: 49381

Bravo AF: 0.507

Asia WGS AF: 0.630 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.67
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs2669010; hg19: chr12-77009060;