rs3757846

Variant names:

• chr7-155456337-C-T
• rs3757846
• ENST00000419225.1:n.110+653G>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+653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,208 control chromosomes in the GnomAD database, including 6,593 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 0.26 (6593 hom., cov: 34)
• Consequence: EN2-DT ENST00000419225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 1 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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+653G>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+653G>A		intron	N/A
	EN2-DT	ENST00000781270.1		n.107+653G>A		intron	N/A
	EN2-DT	ENST00000781271.1		n.86+653G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39926 AN: 152090 Hom.: 6580 Cov.: 34

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.263 AC: 39982 AN: 152208 Hom.: 6593 Cov.: 34 AF XY: 0.265 AC XY: 19701 AN XY: 74418

African (AFR) AF: 0.437 AC: 18119 AN: 41500

American (AMR) AF: 0.216 AC: 3306 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2998 AN: 5168

South Asian (SAS) AF: 0.323 AC: 1561 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1566 AN: 10614

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11173 AN: 68018

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.208 Hom.: 1990

Bravo AF: 0.272

Asia WGS AF: 0.429 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.78
DANN	Benign	0.80
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3757846; hg19: chr7-155249032;