chr1-71638764-C-T

Position:

• chr1-71638764-C-T

Variant summary

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

The NM_173808.3(NEGR1):​c.668-27618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,696 control chromosomes in the GnomAD database, including 5,881 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 0.25 (5881 hom., cov: 31)
• Consequence: NEGR1 NM_173808.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

Genes affected

NEGR1 (HGNC:17302): (neuronal growth regulator 1) Predicted to act upstream of or within several processes, including feeding behavior; locomotory behavior; and positive regulation of neuron projection development. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEGR1	NM_173808.3	c.668-27618G>A		intron_variant		ENST00000357731.10
NEGR1	XM_011541200.4	c.668-27618G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEGR1	ENST00000357731.10	c.668-27618G>A		intron_variant		1	NM_173808.3	P1
NEGR1	ENST00000306821.3	c.284-27618G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38124 AN: 151576 Hom.: 5882 Cov.: 31

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.251 AC: 38126 AN: 151696 Hom.: 5881 Cov.: 31 AF XY: 0.254 AC XY: 18835 AN XY: 74086

Gnomad4 AFR AF: 0.0592

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.279

Alfa AF: 0.309 Hom.: 15830

Bravo AF: 0.244

Asia WGS AF: 0.355 AC: 1232 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	2.0
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041676; hg19: chr1-72104447;