chr4-112518056-C-G

Position:

• chr4-112518056-C-G

Variant summary

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

The XR_007058231.1(LOC124900760):​n.484C>G 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 0.47 in 151,968 control chromosomes in the GnomAD database, including 16,961 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 0.47 (16961 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LOC124900760 XR_007058231.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893

Genes affected

LOC124900760 (HGNC:):

NEUROG2-AS1 (HGNC:40656): (NEUROG2 and ZGRF1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900760	XR_007058231.1	n.484C>G		non_coding_transcript_exon_variant	2/2
NEUROG2-AS1	NR_161159.1	n.262+2416C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEUROG2-AS1	ENST00000504009.1	n.210+2416C>G		intron_variant, non_coding_transcript_variant		3
NEUROG2-AS1	ENST00000506057.1	n.505C>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71415 AN: 151848 Hom.: 16953 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 EAS exome AF: 0.500

GnomAD4 genome AF: 0.470 AC: 71457 AN: 151966 Hom.: 16961 Cov.: 32 AF XY: 0.471 AC XY: 35002 AN XY: 74264

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.447

Alfa AF: 0.305 Hom.: 703

Bravo AF: 0.468

Asia WGS AF: 0.480 AC: 1665 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs701760; hg19: chr4-113439212;