chr17-49514247-T-G

Variant names:

• chr17-49514247-T-G
• rs734194
• NM_002507.4:c.*1238T>G

Variant summary

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

The NM_002507.4(NGFR):​c.*1238T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0987 in 159,724 control chromosomes in the GnomAD database, including 927 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 0.098 (859 hom., cov: 33)
  • Exomes 𝑓: 0.12 (68 hom.)
• Consequence: NGFR NM_002507.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 32 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGFR	NM_002507.4	MANE Select	c.*1238T>G		3_prime_UTR	Exon 6 of 6	NP_002498.1
	NGFR-AS1	NR_103773.1		n.247-3134A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NGFR	ENST00000172229.8	TSL:1 MANE Select	c.*1238T>G		3_prime_UTR	Exon 6 of 6	ENSP00000172229.3
	NGFR-AS1	ENST00000514506.1	TSL:2	n.247-3134A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 14893 AN: 152122 Hom.: 860 Cov.: 33

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0885

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0963

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0961

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.115 AC: 861 AN: 7484 Hom.: 68 Cov.: 0 AF XY: 0.113 AC XY: 435 AN XY: 3854

African (AFR) AF: 0.0455 AC: 8 AN: 176

American (AMR) AF: 0.0794 AC: 10 AN: 126

Ashkenazi Jewish (ASJ) AF: 0.0577 AC: 9 AN: 156

East Asian (EAS) AF: 0.251 AC: 241 AN: 962

South Asian (SAS) AF: 0.0893 AC: 5 AN: 56

European-Finnish (FIN) AF: 0.0854 AC: 83 AN: 972

Middle Eastern (MID) AF: 0.104 AC: 5 AN: 48

European-Non Finnish (NFE) AF: 0.101 AC: 468 AN: 4626

Other (OTH) AF: 0.0884 AC: 32 AN: 362

GnomAD4 genome AF: 0.0978 AC: 14896 AN: 152240 Hom.: 859 Cov.: 33 AF XY: 0.0976 AC XY: 7265 AN XY: 74430

African (AFR) AF: 0.0918 AC: 3815 AN: 41558

American (AMR) AF: 0.0884 AC: 1352 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3472

East Asian (EAS) AF: 0.248 AC: 1278 AN: 5158

South Asian (SAS) AF: 0.0698 AC: 337 AN: 4828

European-Finnish (FIN) AF: 0.0963 AC: 1022 AN: 10612

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0962 AC: 6539 AN: 68002

Other (OTH) AF: 0.109 AC: 231 AN: 2110

Alfa AF: 0.0965 Hom.: 883

Bravo AF: 0.101

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs734194; hg19: chr17-47591609;