chr1-209553912-T-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

ENSG00000224260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424696.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224260	ENST00000424696.6	TSL:2	n.215-7773A>T		intron	N/A
	ENSG00000224260	ENST00000782098.1		n.337-12483A>T		intron	N/A
	ENSG00000224260	ENST00000782099.1		n.376-7773A>T		intron	N/A

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

African (AFR) AF: 0.320 AC: 13259 AN: 41478

American (AMR) AF: 0.425 AC: 6499 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1781 AN: 3472

East Asian (EAS) AF: 0.0954 AC: 494 AN: 5180

South Asian (SAS) AF: 0.467 AC: 2256 AN: 4826

European-Finnish (FIN) AF: 0.589 AC: 6218 AN: 10564

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39254 AN: 67992

Other (OTH) AF: 0.491 AC: 1035 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs12130212; hg19: chr1-209727257;