rs624786

Positions:

• chr11-74982984-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047426298.1(NEU3):​c.-1451T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,752 control chromosomes in the GnomAD database, including 13,301 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 0.41 (13301 hom., cov: 31)
• Consequence: NEU3 XM_047426298.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

NEU3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEU3	XM_047426298.1	c.-1451T>G		5_prime_UTR_variant	1/4
NEU3	XM_047426304.1	c.-1451T>G		5_prime_UTR_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61496 AN: 151634 Hom.: 13306 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.405 AC: 61502 AN: 151752 Hom.: 13301 Cov.: 31 AF XY: 0.402 AC XY: 29779 AN XY: 74132

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.433

Alfa AF: 0.466 Hom.: 8082

Bravo AF: 0.387

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.0
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs624786; hg19: chr11-74694029;