2-239824024-A-G

Variant names:

• chr2-239824024-A-G
• rs4852140
• ENST00000650712.1:n.2782A>G

Variant summary

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

The ENST00000650712.1(ENSG00000220256):​n.2782A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,120 control chromosomes in the GnomAD database, including 43,015 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 0.75 (43015 hom., cov: 34)
• Consequence: ENSG00000220256 ENST00000650712.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 7 publications found

Genes affected

ENSG00000220256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650712.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000220256	ENST00000650712.1		n.2782A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113808 AN: 152002 Hom.: 43001 Cov.: 34

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.748 AC: 113857 AN: 152120 Hom.: 43015 Cov.: 34 AF XY: 0.746 AC XY: 55518 AN XY: 74374

African (AFR) AF: 0.742 AC: 30779 AN: 41504

American (AMR) AF: 0.716 AC: 10939 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2349 AN: 3472

East Asian (EAS) AF: 0.447 AC: 2309 AN: 5166

South Asian (SAS) AF: 0.637 AC: 3076 AN: 4826

European-Finnish (FIN) AF: 0.822 AC: 8695 AN: 10580

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53221 AN: 67972

Other (OTH) AF: 0.742 AC: 1567 AN: 2112

Alfa AF: 0.768 Hom.: 171111

Bravo AF: 0.741

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4852140; hg19: chr2-240745718; COSMIC: COSV107166637;