chr6-136988049-G-A

Variant names:

• chr6-136988049-G-A
• rs1744062
• ENST00000418699.1:n.360+2013C>T

Variant summary

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

The ENST00000418699.1(NHEG1):​n.360+2013C>T variant causes a intron 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 ENST00000418699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 6 publications found

Genes affected

NHEG1 (HGNC:56731): (neuroblastoma highly expressed DDX5 stabilizing lncRNA 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 (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418699.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NHEG1	NR_027994.1		n.365+2005C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NHEG1	ENST00000418699.1	TSL:1	n.360+2013C>T		intron	N/A
	NHEG1	ENST00000432330.5	TSL:1	n.368+2005C>T		intron	N/A

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

African (AFR) AF: 0.440 AC: 18236 AN: 41440

American (AMR) AF: 0.451 AC: 6891 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5172

South Asian (SAS) AF: 0.337 AC: 1623 AN: 4818

European-Finnish (FIN) AF: 0.439 AC: 4634 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36996 AN: 67970

Other (OTH) AF: 0.488 AC: 1028 AN: 2106

Alfa AF: 0.516 Hom.: 13044

Bravo AF: 0.478

Asia WGS AF: 0.345 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1744062; hg19: chr6-137309186;