Genetic Variant NGFR:c.*1332T>C (chr17-49514341-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.*1332T>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 0.589 in 153,346 control chromosomes in the GnomAD database, including 26,728 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 0.59 ( 26496 hom., cov: 33)

Exomes 𝑓: 0.63 ( 232 hom. )

Consequence

NGFR
NM_002507.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.25

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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.671 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.*1332T>C		3_prime_UTR	Exon 6 of 6	NP_002498.1
	NGFR-AS1	NR_103773.1		n.247-3228A>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.*1332T>C		3_prime_UTR	Exon 6 of 6	ENSP00000172229.3
	NGFR-AS1	ENST00000514506.1	TSL:2	n.247-3228A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89485

AN:

151972

Hom.:

26480

Cov.:

show subpopulations

Gnomad AFR

AF:

0.628

Gnomad AMI

AF:

0.535

Gnomad AMR

AF:

0.532

Gnomad ASJ

AF:

0.486

Gnomad EAS

AF:

0.608

Gnomad SAS

AF:

0.690

Gnomad FIN

AF:

0.554

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.581

Gnomad OTH

AF:

0.577

GnomAD4 exome

AF:

0.625

AC:

785

AN:

1256

Hom.:

232

Cov.:

AF XY:

0.613

AC XY:

435

AN XY:

710

show subpopulations

African (AFR)

AF:

0.659

AC:

AN:

American (AMR)

AF:

0.563

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.450

AC:

AN:

East Asian (EAS)

AF:

0.614

AC:

AN:

114

South Asian (SAS)

AF:

0.700

AC:

AN:

European-Finnish (FIN)

AF:

0.632

AC:

AN:

136

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.625

AC:

525

AN:

840

Other (OTH)

AF:

0.686

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

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:

0.589

AC:

89542

AN:

152090

Hom.:

26496

Cov.:

AF XY:

0.589

AC XY:

43753

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.628

AC:

26044

AN:

41470

American (AMR)

AF:

0.532

AC:

8142

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.486

AC:

1689

AN:

3472

East Asian (EAS)

AF:

0.608

AC:

3140

AN:

5168

South Asian (SAS)

AF:

0.690

AC:

3331

AN:

4826

European-Finnish (FIN)

AF:

0.554

AC:

5854

AN:

10558

Middle Eastern (MID)

AF:

0.398

AC:

117

AN:

294

European-Non Finnish (NFE)

AF:

0.581

AC:

39520

AN:

67982

Other (OTH)

AF:

0.577

AC:

1219

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1913

3825

5738

7650

9563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.576

Hom.:

24832

Bravo

AF:

0.587

Asia WGS

AF:

0.655

AC:

2279

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.11

(source)

DANN

Benign

0.52

PhyloP100

-2.2

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