1-115339882-T-C

Position:

• chr1-115339882-T-C

Variant summary

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

The ENST00000425449.1(NGF-AS1):​n.208-25788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,174 control chromosomes in the GnomAD database, including 7,174 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 0.27 (7174 hom., cov: 33)
• Consequence: NGF-AS1 ENST00000425449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

Genes affected

NGF-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NGF-AS1	NR_157569.1	n.208-25788T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NGF-AS1	ENST00000425449.1	n.208-25788T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40872 AN: 152056 Hom.: 7163 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.269 AC: 40930 AN: 152174 Hom.: 7174 Cov.: 33 AF XY: 0.266 AC XY: 19760 AN XY: 74414

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.232

Alfa AF: 0.179 Hom.: 1716

Bravo AF: 0.276

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811014; hg19: chr1-115882503;