1-115277977-T-C

Variant names:

• chr1-115277977-T-C
• rs11102915
• ENST00000649888.1:n.215-1343A>G

Variant summary

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

The ENST00000649888.1(ENSG00000285698):​n.215-1343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 152,094 control chromosomes in the GnomAD database, including 20,593 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 0.49 (20593 hom., cov: 33)
• Consequence: ENSG00000285698 ENST00000649888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 2 publications found

Genes affected

ENSG00000285698 (HGNC:):

NGF-AS1 (HGNC:53922): (NGF antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285698	ENST00000649888.1	n.215-1343A>G		intron_variant	Intron 1 of 3
NGF-AS1	ENST00000793538.1	n.227+2818T>C		intron_variant	Intron 2 of 4
NGF-AS1	ENST00000793543.1	n.370-3536T>C		intron_variant	Intron 1 of 1
ENSG00000285698	ENST00000793772.1	n.104+939A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74921 AN: 151976 Hom.: 20548 Cov.: 33

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.493 AC: 75017 AN: 152094 Hom.: 20593 Cov.: 33 AF XY: 0.494 AC XY: 36705 AN XY: 74340

African (AFR) AF: 0.746 AC: 30925 AN: 41482

American (AMR) AF: 0.459 AC: 7025 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3468

East Asian (EAS) AF: 0.541 AC: 2801 AN: 5178

South Asian (SAS) AF: 0.540 AC: 2593 AN: 4802

European-Finnish (FIN) AF: 0.327 AC: 3462 AN: 10576

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25219 AN: 67984

Other (OTH) AF: 0.468 AC: 986 AN: 2106

Alfa AF: 0.457 Hom.: 2251

Bravo AF: 0.511

Asia WGS AF: 0.553 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.52
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs11102915; hg19: chr1-115820598;