ENST00000839742.1:n.164+1886T>G

Variant names:

• chr2-25983386-T-G
• rs2384319
• ENST00000839742.1:n.164+1886T>G

Variant summary

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

The ENST00000839742.1(ENSG00000309231):​n.164+1886T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,236 control chromosomes in the GnomAD database, including 4,267 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 0.16 (4267 hom., cov: 33)
• Consequence: ENSG00000309231 ENST00000839742.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337
• Publications: 9 publications found

Genes affected

ENSG00000309231 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839742.1. 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
	ENSG00000309231	ENST00000839742.1		n.164+1886T>G		intron	N/A
	ENSG00000309231	ENST00000839743.1		n.159+1645T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24703 AN: 152118 Hom.: 4266 Cov.: 33

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0997

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.162 AC: 24720 AN: 152236 Hom.: 4267 Cov.: 33 AF XY: 0.177 AC XY: 13208 AN XY: 74440

African (AFR) AF: 0.0861 AC: 3578 AN: 41560

American (AMR) AF: 0.354 AC: 5401 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4734 AN: 5170

South Asian (SAS) AF: 0.259 AC: 1252 AN: 4826

European-Finnish (FIN) AF: 0.203 AC: 2152 AN: 10596

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0996 AC: 6778 AN: 68022

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.124 Hom.: 9755

Bravo AF: 0.174

Asia WGS AF: 0.503 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2384319; hg19: chr2-26206255;