rs12130212

Positions:

• chr1-209553912-T-A

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, non coding transcript 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: ENST00000424696.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000424696.6	n.215-7773A>T		intron_variant, non_coding_transcript_variant		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;