rs1744062

Positions:

• chr6-136988049-G-A

Variant summary

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

The NR_027994.1(NHEG1):​n.365+2005C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,002 control chromosomes in the GnomAD database, including 17,861 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 0.48 (17861 hom., cov: 32)
• Consequence: NHEG1 NR_027994.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

Genes affected

NHEG1 (HGNC:56731): (neuroblastoma highly expressed DDX5 stabilizing lncRNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NHEG1	NR_027994.1	n.365+2005C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NHEG1	ENST00000418699.1	n.360+2013C>T		intron_variant, non_coding_transcript_variant		1
NHEG1	ENST00000432330.5	n.368+2005C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72474 AN: 151882 Hom.: 17841 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.477 AC: 72551 AN: 152002 Hom.: 17861 Cov.: 32 AF XY: 0.467 AC XY: 34676 AN XY: 74300

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.488

Alfa AF: 0.514 Hom.: 11891

Bravo AF: 0.478

Asia WGS AF: 0.345 AC: 1202 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	1.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1744062; hg19: chr6-137309186;