rs1345514

Variant names:

• chr7-155456455-C-T
• rs1345514
• ENST00000419225.1:n.110+535G>A

Variant summary

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

The ENST00000419225.1(EN2-DT):​n.110+535G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,046 control chromosomes in the GnomAD database, including 7,962 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 0.29 (7962 hom., cov: 33)
• Consequence: EN2-DT ENST00000419225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 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+535G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EN2-DT	ENST00000419225.1	TSL:4	n.110+535G>A		intron	N/A
	EN2-DT	ENST00000781270.1		n.107+535G>A		intron	N/A
	EN2-DT	ENST00000781271.1		n.86+535G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43947 AN: 151928 Hom.: 7957 Cov.: 33

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.0916

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.289 AC: 43963 AN: 152046 Hom.: 7962 Cov.: 33 AF XY: 0.284 AC XY: 21105 AN XY: 74314

African (AFR) AF: 0.0797 AC: 3306 AN: 41496

American (AMR) AF: 0.311 AC: 4747 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1463 AN: 3470

East Asian (EAS) AF: 0.0915 AC: 473 AN: 5172

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4814

European-Finnish (FIN) AF: 0.370 AC: 3907 AN: 10546

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27753 AN: 67944

Other (OTH) AF: 0.316 AC: 667 AN: 2110

Alfa AF: 0.346 Hom.: 5846

Bravo AF: 0.279

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1345514;

hg19: chr7-155249150;