chr1-115271144-C-G

Variant names:

• chr1-115271144-C-G
• rs2057127
• ENST00000649888.1:n.977G>C

Variant summary

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

The ENST00000649888.1(ENSG00000285698):​n.977G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,924 control chromosomes in the GnomAD database, including 12,941 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 (12941 hom., cov: 32)
• Consequence: ENSG00000285698 ENST00000649888.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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.977G>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000285698	ENST00000793772.1	n.553G>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000285698	ENST00000793773.1	n.563G>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62174 AN: 151806 Hom.: 12936 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.409 AC: 62203 AN: 151924 Hom.: 12941 Cov.: 32 AF XY: 0.413 AC XY: 30662 AN XY: 74272

African (AFR) AF: 0.476 AC: 19704 AN: 41408

American (AMR) AF: 0.411 AC: 6270 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1417 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2608 AN: 5146

South Asian (SAS) AF: 0.500 AC: 2410 AN: 4818

European-Finnish (FIN) AF: 0.343 AC: 3623 AN: 10556

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24880 AN: 67942

Other (OTH) AF: 0.401 AC: 846 AN: 2112

Alfa AF: 0.231 Hom.: 459

Bravo AF: 0.415

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.58
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs2057127; hg19: chr1-115813765;