ENST00000725912.1:n.227-719C>G

Variant names:

• chr2-120327131-C-G
• rs934716
• ENST00000725912.1:n.227-719C>G

Variant summary

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

The ENST00000725912.1(ENSG00000235840):​n.227-719C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,094 control chromosomes in the GnomAD database, including 54,075 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 0.84 (54075 hom., cov: 31)
• Consequence: ENSG00000235840 ENST00000725912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 2 publications found

Genes affected

ENSG00000235840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.909 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
ENSG00000235840	ENST00000725912.1	n.227-719C>G		intron_variant	Intron 1 of 1
ENSG00000235840	ENST00000725913.1	n.294-719C>G		intron_variant	Intron 2 of 2
ENSG00000235840	ENST00000725914.1	n.193-719C>G		intron_variant	Intron 1 of 1
ENSG00000235840	ENST00000725915.1	n.293-719C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127168 AN: 151978 Hom.: 54017 Cov.: 31

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.837 AC: 127277 AN: 152094 Hom.: 54075 Cov.: 31 AF XY: 0.833 AC XY: 61969 AN XY: 74352

African (AFR) AF: 0.710 AC: 29426 AN: 41458

American (AMR) AF: 0.891 AC: 13627 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3041 AN: 3468

East Asian (EAS) AF: 0.549 AC: 2826 AN: 5152

South Asian (SAS) AF: 0.867 AC: 4174 AN: 4816

European-Finnish (FIN) AF: 0.858 AC: 9088 AN: 10586

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.916 AC: 62256 AN: 68002

Other (OTH) AF: 0.854 AC: 1803 AN: 2112

Alfa AF: 0.873 Hom.: 6835

Bravo AF: 0.828

Asia WGS AF: 0.744 AC: 2588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.77
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs934716; hg19: chr2-121084707;