rs12122100

Variant names:

• chr1-147037378-T-C
• rs12122100
• ENST00000444082.2:n.988+4018A>G

Variant summary

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

The ENST00000444082.2(ENSG00000227242):​n.988+4018A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,030 control chromosomes in the GnomAD database, including 44,860 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 0.77 (44860 hom., cov: 32)
• Consequence: ENSG00000227242 ENST00000444082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 16 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC728989	NR_024442.2	n.90+5572A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227242	ENST00000444082.2	n.988+4018A>G		intron_variant	Intron 8 of 14	6
ENSG00000310005	ENST00000846524.1	n.388+5572A>G		intron_variant	Intron 1 of 7
ENSG00000310005	ENST00000846525.1	n.123+5572A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116200 AN: 151912 Hom.: 44797 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.765 AC: 116326 AN: 152030 Hom.: 44860 Cov.: 32 AF XY: 0.775 AC XY: 57563 AN XY: 74318

African (AFR) AF: 0.761 AC: 31534 AN: 41462

American (AMR) AF: 0.824 AC: 12589 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2432 AN: 3466

East Asian (EAS) AF: 0.982 AC: 5096 AN: 5188

South Asian (SAS) AF: 0.911 AC: 4385 AN: 4814

European-Finnish (FIN) AF: 0.793 AC: 8384 AN: 10568

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49318 AN: 67942

Other (OTH) AF: 0.772 AC: 1631 AN: 2114

Alfa AF: 0.747 Hom.: 121054

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.16
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12122100; hg19: chr1-146508934;