2-239824024-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000220256 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000220256	ENST00000650712.1	n.2782A>G		non_coding_transcript_exon_variant	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

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.742

Alfa AF: 0.773 Hom.: 63366

Bravo AF: 0.741

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4852140; hg19: chr2-240745718;