17-49514341-T-C

Variant names:

• chr17-49514341-T-C
• rs741072
• NM_002507.4:c.*1332T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NGFR	NM_002507.4	c.*1332T>C		3_prime_UTR_variant	Exon 6 of 6	ENST00000172229.8	NP_002498.1
NGFR-AS1	NR_103773.1	n.247-3228A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NGFR	ENST00000172229.8	c.*1332T>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_002507.4	ENSP00000172229.3
NGFR-AS1	ENST00000514506.1	n.247-3228A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89485 AN: 151972 Hom.: 26480 Cov.: 33

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.: 0 AF XY: 0.613 AC XY: 435 AN XY: 710

Gnomad4 AFR exome AF: 0.659

Gnomad4 AMR exome AF: 0.563

Gnomad4 ASJ exome AF: 0.450

Gnomad4 EAS exome AF: 0.614

Gnomad4 SAS exome AF: 0.700

Gnomad4 FIN exome AF: 0.632

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 0.686

GnomAD4 genome AF: 0.589 AC: 89542 AN: 152090 Hom.: 26496 Cov.: 33 AF XY: 0.589 AC XY: 43753 AN XY: 74320

Gnomad4 AFR AF: 0.628

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.577

Alfa AF: 0.571 Hom.: 15317

Bravo AF: 0.587

Asia WGS AF: 0.655 AC: 2279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.11
DANN	Benign	0.52

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: rs741072; hg19: chr17-47591703; COSMIC: COSV50804960; COSMIC: COSV50804960;