rs1800598

Variant names:

• chr12-5430580-A-G
• rs1800598
• XM_047428901.1:c.-635A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-5430580-A-G
• chr12-5430580-A-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS1

The ENST00000790001.1(ENSG00000256218):​n.18T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000719 in 148,718 control chromosomes in the GnomAD database, including 1 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 0.00072 (1 hom., cov: 30)
• Consequence: ENSG00000256218 ENST00000790001.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 1 publications found

Genes affected

NTF3 (HGNC:8023): (neurotrophin 3) The protein encoded by this gene is a member of the neurotrophin family, that controls survival and differentiation of mammalian neurons. This protein is closely related to both nerve growth factor and brain-derived neurotrophic factor. It may be involved in the maintenance of the adult nervous system, and may affect development of neurons in the embryo when it is expressed in human placenta. NTF3-deficient mice generated by gene targeting display severe movement defects of the limbs. The mature peptide of this protein is identical in all mammals examined including human, pig, rat and mouse. [provided by RefSeq, Jul 2008]

ENSG00000256218 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000719 (107/148718) while in subpopulation EAS AF = 0.0199 (100/5032). AF 95% confidence interval is 0.0167. There are 1 homozygotes in GnomAd4. There are 61 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790001.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256218	ENST00000790001.1		n.18T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000256218	ENST00000790002.1		n.188T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000256218	ENST00000790004.1		n.9T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.000733 AC: 109 AN: 148612 Hom.: 1 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.000864

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000448

Gnomad OTH AF: 0.000493

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.000719 AC: 107 AN: 148718 Hom.: 1 Cov.: 30 AF XY: 0.000841 AC XY: 61 AN XY: 72570

African (AFR) AF: 0.00 AC: 0 AN: 40284

American (AMR) AF: 0.00 AC: 0 AN: 14970

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3420

East Asian (EAS) AF: 0.0199 AC: 100 AN: 5032

South Asian (SAS) AF: 0.000649 AC: 3 AN: 4624

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10242

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000448 AC: 3 AN: 66906

Other (OTH) AF: 0.000488 AC: 1 AN: 2050

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.000926

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.0
DANN	Benign	0.73
PhyloP100		-0.052

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1800598; hg19: chr12-5539746;