16-56386682-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001144.6(AMFR):​c.1277-660C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,006 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 33)

Consequence

AMFR
NM_001144.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.786
Variant links:
Genes affected
AMFR (HGNC:463): (autocrine motility factor receptor) This locus encodes a glycosylated transmembrane receptor. Its ligand, autocrine motility factor, is a tumor motility-stimulating protein secreted by tumor cells. The encoded receptor is also a member of the E3 ubiquitin ligase family of proteins. It catalyzes ubiquitination and endoplasmic reticulum-associated degradation of specific proteins. [provided by RefSeq, Feb 2012]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AMFRNM_001144.6 linkc.1277-660C>G intron_variant Intron 9 of 13 ENST00000290649.10 NP_001135.3 Q9UKV5
AMFRNM_001323512.2 linkc.1373-660C>G intron_variant Intron 10 of 14 NP_001310441.1 Q9UKV5
AMFRNM_001323511.2 linkc.992-660C>G intron_variant Intron 9 of 13 NP_001310440.1 A0A024R6R5
AMFRXM_005255890.5 linkc.992-660C>G intron_variant Intron 9 of 13 XP_005255947.1 A0A024R6R5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AMFRENST00000290649.10 linkc.1277-660C>G intron_variant Intron 9 of 13 1 NM_001144.6 ENSP00000290649.5 Q9UKV5
AMFRENST00000492830.5 linkc.245-660C>G intron_variant Intron 2 of 6 2 ENSP00000473636.1 R4GNG2
AMFRENST00000567738.1 linkc.518-660C>G intron_variant Intron 4 of 7 5 ENSP00000456288.1 H3BRK9
AMFRENST00000568762.1 linkn.44-660C>G intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
152006
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
152006
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
74204
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.068
DANN
Benign
0.38

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2440468; hg19: chr16-56420594; API