rs734194

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-49514247-T-A
• chr17-49514247-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002507.4(NGFR):​c.*1238T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NGFR	NM_002507.4	c.*1238T>A		3_prime_UTR_variant	Exon 6 of 6	ENST00000172229.8	NP_002498.1
NGFR-AS1	NR_103773.1	n.247-3134A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NGFR	ENST00000172229.8	c.*1238T>A		3_prime_UTR_variant	Exon 6 of 6	1	NM_002507.4	ENSP00000172229.3
NGFR-AS1	ENST00000514506.1	n.247-3134A>T		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 7510 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3860

African (AFR) AF: 0.00 AC: 0 AN: 178

American (AMR) AF: 0.00 AC: 0 AN: 126

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 156

East Asian (EAS) AF: 0.00 AC: 0 AN: 966

South Asian (SAS) AF: 0.00 AC: 0 AN: 56

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 976

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 48

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4640

Other (OTH) AF: 0.00 AC: 0 AN: 364

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		0.34

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;