rs12130212

Variant names:

• chr1-209553912-T-A
• rs12130212
• ENST00000424696.6:n.215-7773A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000424696.6(ENSG00000224260):​n.215-7773A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,114 control chromosomes in the GnomAD database, including 18,169 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 0.47 (18169 hom., cov: 32)
• Consequence: ENSG00000224260 ENST00000424696.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

ENSG00000224260 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 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
ENSG00000224260	ENST00000424696.6	n.215-7773A>T		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71349 AN: 151996 Hom.: 18173 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.469 AC: 71361 AN: 152114 Hom.: 18169 Cov.: 32 AF XY: 0.468 AC XY: 34805 AN XY: 74372

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.491

Alfa AF: 0.537 Hom.: 12822

Bravo AF: 0.444

Asia WGS AF: 0.254 AC: 889 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12130212; hg19: chr1-209727257;