2-27412596-A-G

Variant names:

• chr2-27412596-A-G
• rs1728918
• ENST00000756153.1:n.477-44A>G

Variant summary

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

The ENST00000756153.1(ENSG00000298520):​n.477-44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,810 control chromosomes in the GnomAD database, including 47,285 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 0.78 (47285 hom., cov: 29)
• Consequence: ENSG00000298520 ENST00000756153.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862
• Publications: 58 publications found

Genes affected

ENSG00000298520 (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 (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756153.1. 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
	ENSG00000298520	ENST00000756153.1		n.477-44A>G		intron	N/A
	ENSG00000298520	ENST00000756154.1		n.579-44A>G		intron	N/A
	ENSG00000298520	ENST00000756155.1		n.395-44A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118696 AN: 151692 Hom.: 47220 Cov.: 29

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.783 AC: 118827 AN: 151810 Hom.: 47285 Cov.: 29 AF XY: 0.784 AC XY: 58161 AN XY: 74194

African (AFR) AF: 0.933 AC: 38651 AN: 41416

American (AMR) AF: 0.744 AC: 11301 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3957 AN: 5160

South Asian (SAS) AF: 0.848 AC: 4053 AN: 4782

European-Finnish (FIN) AF: 0.765 AC: 8059 AN: 10534

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48273 AN: 67944

Other (OTH) AF: 0.761 AC: 1605 AN: 2108

Alfa AF: 0.737 Hom.: 116518

Bravo AF: 0.787

Asia WGS AF: 0.844 AC: 2932 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	1.1
DANN	Benign	0.64
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1728918; hg19: chr2-27635463;