chr2-212959321-A-G

Variant names:

• chr2-212959321-A-G
• rs12619285
• ENST00000415387.1:n.82-55878T>C

Variant summary

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

The ENST00000415387.1(ENSG00000273118):​n.82-55878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,000 control chromosomes in the GnomAD database, including 8,384 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 0.32 (8384 hom., cov: 32)
• Consequence: ENSG00000273118 ENST00000415387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 39 publications found

Genes affected

ENSG00000273118 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273118	ENST00000415387.1	TSL:3	n.82-55878T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48078 AN: 151882 Hom.: 8376 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.317 AC: 48117 AN: 152000 Hom.: 8384 Cov.: 32 AF XY: 0.322 AC XY: 23907 AN XY: 74290

African (AFR) AF: 0.336 AC: 13946 AN: 41468

American (AMR) AF: 0.463 AC: 7064 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 781 AN: 3462

East Asian (EAS) AF: 0.658 AC: 3389 AN: 5148

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3046 AN: 10584

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.263 AC: 17856 AN: 67940

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.288 Hom.: 32421

Bravo AF: 0.338

Asia WGS AF: 0.399 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.7
DANN	Benign	0.62
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12619285;

hg19: chr2-213824045;