rs34808376

Positions:

• chr7-155456016-A-AGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000419225.1(EN2-DT):​n.110+972_110+973dupGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (19443 hom., cov: 0)
• Consequence: EN2-DT ENST00000419225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

EN2-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EN2-DT	NR_186580.1	n.129+972_129+973dupGC		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EN2-DT	ENST00000419225.1	n.110+972_110+973dupGC		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74901 AN: 151610 Hom.: 19425 Cov.: 0

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.494 AC: 74958 AN: 151728 Hom.: 19443 Cov.: 0 AF XY: 0.498 AC XY: 36896 AN XY: 74150

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.469

Alfa AF: 0.460 Hom.: 1740

Bravo AF: 0.497

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34808376; hg19: chr7-155248711;