rs12122453

Variant names:

• chr1-147032561-G-C
• rs12122453
• ENST00000444082.2:n.989-1423C>G

Variant summary

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

The ENST00000444082.2(ENSG00000227242):​n.989-1423C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,070 control chromosomes in the GnomAD database, including 30,116 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 0.63 (30116 hom., cov: 32)
• Consequence: ENSG00000227242 ENST00000444082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 4 publications found

Genes affected

ENSG00000227242 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC728989	NR_024442.2	n.91-7637C>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227242	ENST00000444082.2	n.989-1423C>G		intron_variant	Intron 8 of 14	6
ENSG00000310005	ENST00000846524.1	n.389-1421C>G		intron_variant	Intron 1 of 7
ENSG00000310005	ENST00000846525.1	n.124-1421C>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95017 AN: 151950 Hom.: 30069 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.626 AC: 95130 AN: 152070 Hom.: 30116 Cov.: 32 AF XY: 0.637 AC XY: 47350 AN XY: 74326

African (AFR) AF: 0.598 AC: 24786 AN: 41474

American (AMR) AF: 0.683 AC: 10433 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3468

East Asian (EAS) AF: 0.864 AC: 4471 AN: 5172

South Asian (SAS) AF: 0.729 AC: 3513 AN: 4820

European-Finnish (FIN) AF: 0.714 AC: 7534 AN: 10546

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40345 AN: 67998

Other (OTH) AF: 0.624 AC: 1317 AN: 2110

Alfa AF: 0.616 Hom.: 3562

Bravo AF: 0.626

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs12122453; hg19: chr1-146504114;