ENST00000419225.1:n.110+2072_110+2080delGATGCGGGG

Variant names:

• chr7-155454909-GCCCCGCATC-G
• rs6150410
• ENST00000419225.1:n.110+2072_110+2080delGATGCGGGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000419225.1(EN2-DT):​n.110+2072_110+2080delGATGCGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,916 control chromosomes in the GnomAD database, including 7,301 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7301 hom., cov: 22)
• Consequence: EN2-DT ENST00000419225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 1 publications found

Genes affected

EN2-DT (HGNC:55659): (EN2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419225.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EN2-DT	NR_186580.1		n.129+2072_129+2080delGATGCGGGG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EN2-DT	ENST00000419225.1	TSL:4	n.110+2072_110+2080delGATGCGGGG		intron	N/A
	EN2-DT	ENST00000781270.1		n.107+2072_107+2080delGATGCGGGG		intron	N/A
	EN2-DT	ENST00000781271.1		n.86+2072_86+2080delGATGCGGGG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42223 AN: 151798 Hom.: 7295 Cov.: 22

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.278 AC: 42242 AN: 151916 Hom.: 7301 Cov.: 22 AF XY: 0.273 AC XY: 20308 AN XY: 74280

African (AFR) AF: 0.0759 AC: 3153 AN: 41556

American (AMR) AF: 0.304 AC: 4645 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1451 AN: 3458

East Asian (EAS) AF: 0.0899 AC: 464 AN: 5160

South Asian (SAS) AF: 0.201 AC: 971 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3823 AN: 10570

Middle Eastern (MID) AF: 0.390 AC: 113 AN: 290

European-Non Finnish (NFE) AF: 0.390 AC: 26460 AN: 67784

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.328 Hom.: 1095

Bravo AF: 0.270

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6150410; hg19: chr7-155247604;