rs12142280

Variant names:

• chr1-172895512-T-A
• rs12142280
• ENST00000432694.2:n.224-108770T>A

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.224-108770T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,086 control chromosomes in the GnomAD database, including 3,497 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 0.20 (3497 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 7 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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
ENSG00000224000	ENST00000432694.2	n.224-108770T>A		intron_variant	Intron 1 of 4	3
ENSG00000224000	ENST00000717047.1	n.354-4454T>A		intron_variant	Intron 2 of 4
ENSG00000224000	ENST00000717048.1	n.323+11813T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31049 AN: 151968 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.204 AC: 31065 AN: 152086 Hom.: 3497 Cov.: 32 AF XY: 0.203 AC XY: 15125 AN XY: 74350

African (AFR) AF: 0.297 AC: 12290 AN: 41448

American (AMR) AF: 0.127 AC: 1945 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.00501 AC: 26 AN: 5190

South Asian (SAS) AF: 0.200 AC: 964 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2120 AN: 10582

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.184 AC: 12475 AN: 67972

Other (OTH) AF: 0.188 AC: 398 AN: 2112

Alfa AF: 0.198 Hom.: 358

Bravo AF: 0.201

Asia WGS AF: 0.122 AC: 426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.6
DANN	Benign	0.40
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12142280; hg19: chr1-172864652;