ENST00000726607.1:n.342-1409A>C

Variant names:

• chr2-127133851-A-C
• rs4663105
• ENST00000726607.1:n.342-1409A>C

Variant summary

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

The ENST00000726607.1(ENSG00000294899):​n.342-1409A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,642 control chromosomes in the GnomAD database, including 16,715 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 0.46 (16715 hom., cov: 30)
• Consequence: ENSG00000294899 ENST00000726607.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 52 publications found

Genes affected

ENSG00000294899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726607.1. 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
	ENSG00000294899	ENST00000726607.1		n.342-1409A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70057 AN: 151522 Hom.: 16652 Cov.: 30

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.463 AC: 70188 AN: 151642 Hom.: 16715 Cov.: 30 AF XY: 0.462 AC XY: 34258 AN XY: 74108

African (AFR) AF: 0.572 AC: 23641 AN: 41326

American (AMR) AF: 0.464 AC: 7070 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2334 AN: 5128

South Asian (SAS) AF: 0.475 AC: 2278 AN: 4800

European-Finnish (FIN) AF: 0.399 AC: 4174 AN: 10470

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27929 AN: 67888

Other (OTH) AF: 0.425 AC: 895 AN: 2104

Alfa AF: 0.443 Hom.: 1906

Bravo AF: 0.470

Asia WGS AF: 0.539 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.28
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4663105; hg19: chr2-127891427;