Genetic Variant NM_002507.4:c.*1319T>C (chr17-49514328-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002507.4(NGFR):c.*1319T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 154,072 control chromosomes in the GnomAD database, including 21,672 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 0.52 ( 21345 hom., cov: 33)

Exomes 𝑓: 0.57 ( 327 hom. )

Consequence

NGFR
NM_002507.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.834

Publications

16 publications found

Variant links:

Genes affected

NGFR (HGNC:7809): (nerve growth factor receptor) Nerve growth factor receptor contains an extracellular domain containing four 40-amino acid repeats with 6 cysteine residues at conserved positions followed by a serine/threonine-rich region, a single transmembrane domain, and a 155-amino acid cytoplasmic domain. The cysteine-rich region contains the nerve growth factor binding domain. [provided by RefSeq, Jul 2008]

NGFR links:

NGFR-AS1 (HGNC:55555): (NGFR antisense RNA 1)

NGFR-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002507.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGFR	NM_002507.4	MANE Select	c.*1319T>C		3_prime_UTR	Exon 6 of 6	NP_002498.1	P08138-1
	NGFR-AS1	NR_103773.1		n.247-3215A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGFR	ENST00000172229.8	TSL:1 MANE Select	c.*1319T>C		3_prime_UTR	Exon 6 of 6	ENSP00000172229.3	P08138-1
	NGFR-AS1	ENST00000514506.1	TSL:2	n.247-3215A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.524

AC:

79602

AN:

151934

Hom.:

21334

Cov.:

show subpopulations

Gnomad AFR

AF:

0.418

Gnomad AMI

AF:

0.528

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.554

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.576

Gnomad OTH

AF:

0.521

GnomAD4 exome

AF:

0.572

AC:

1155

AN:

2020

Hom.:

327

Cov.:

AF XY:

0.562

AC XY:

629

AN XY:

1120

show subpopulations

African (AFR)

AF:

0.389

AC:

AN:

American (AMR)

AF:

0.571

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.200

AC:

AN:

East Asian (EAS)

AF:

0.624

AC:

131

AN:

210

South Asian (SAS)

AF:

0.857

AC:

AN:

European-Finnish (FIN)

AF:

0.542

AC:

129

AN:

238

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.584

AC:

765

AN:

1310

Other (OTH)

AF:

0.583

AC:

AN:

108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.524

AC:

79641

AN:

152052

Hom.:

21345

Cov.:

AF XY:

0.526

AC XY:

39116

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.418

AC:

17319

AN:

41464

American (AMR)

AF:

0.499

AC:

7624

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

1566

AN:

3472

East Asian (EAS)

AF:

0.609

AC:

3140

AN:

5160

South Asian (SAS)

AF:

0.684

AC:

3306

AN:

4832

European-Finnish (FIN)

AF:

0.554

AC:

5853

AN:

10560

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.576

AC:

39145

AN:

67956

Other (OTH)

AF:

0.520

AC:

1100

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1960

3920

5879

7839

9799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

714

1428

2142

2856

3570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.555

Hom.:

86371

Bravo

AF:

0.511

Asia WGS

AF:

0.639

AC:

2223

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.38

(source)

DANN

Benign

0.29

PhyloP100

-0.83

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over