16-56362574-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001144.6(AMFR):​c.*335G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 585,466 control chromosomes in the GnomAD database, including 92,818 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 ( 27404 hom., cov: 32)
Exomes 𝑓: 0.54 ( 65414 hom. )

Consequence

AMFR
NM_001144.6 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.341
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AMFRNM_001144.6 linkc.*335G>A 3_prime_UTR_variant Exon 14 of 14 ENST00000290649.10 NP_001135.3 Q9UKV5
AMFRNM_001323512.2 linkc.*335G>A 3_prime_UTR_variant Exon 15 of 15 NP_001310441.1 Q9UKV5
AMFRNM_001323511.2 linkc.*335G>A 3_prime_UTR_variant Exon 14 of 14 NP_001310440.1 A0A024R6R5
AMFRXM_005255890.5 linkc.*335G>A 3_prime_UTR_variant Exon 14 of 14 XP_005255947.1 A0A024R6R5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AMFRENST00000290649 linkc.*335G>A 3_prime_UTR_variant Exon 14 of 14 1 NM_001144.6 ENSP00000290649.5 Q9UKV5
AMFRENST00000492830 linkc.*335G>A 3_prime_UTR_variant Exon 7 of 7 2 ENSP00000473636.1 R4GNG2
AMFRENST00000566757.1 linkn.1272G>A non_coding_transcript_exon_variant Exon 1 of 1 6
AMFRENST00000568325.1 linkn.679G>A non_coding_transcript_exon_variant Exon 2 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.587
AC:
89100
AN:
151844
Hom.:
27378
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.762
Gnomad AMI
AF:
0.580
Gnomad AMR
AF:
0.549
Gnomad ASJ
AF:
0.530
Gnomad EAS
AF:
0.436
Gnomad SAS
AF:
0.605
Gnomad FIN
AF:
0.392
Gnomad MID
AF:
0.472
Gnomad NFE
AF:
0.533
Gnomad OTH
AF:
0.563
GnomAD3 exomes
AF:
0.545
AC:
126233
AN:
231608
Hom.:
35236
AF XY:
0.544
AC XY:
69528
AN XY:
127766
show subpopulations
Gnomad AFR exome
AF:
0.772
Gnomad AMR exome
AF:
0.567
Gnomad ASJ exome
AF:
0.537
Gnomad EAS exome
AF:
0.418
Gnomad SAS exome
AF:
0.611
Gnomad FIN exome
AF:
0.406
Gnomad NFE exome
AF:
0.528
Gnomad OTH exome
AF:
0.528
GnomAD4 exome
AF:
0.543
AC:
235598
AN:
433504
Hom.:
65414
Cov.:
2
AF XY:
0.547
AC XY:
133340
AN XY:
243590
show subpopulations
Gnomad4 AFR exome
AF:
0.764
Gnomad4 AMR exome
AF:
0.567
Gnomad4 ASJ exome
AF:
0.532
Gnomad4 EAS exome
AF:
0.465
Gnomad4 SAS exome
AF:
0.611
Gnomad4 FIN exome
AF:
0.404
Gnomad4 NFE exome
AF:
0.528
Gnomad4 OTH exome
AF:
0.532
GnomAD4 genome
AF:
0.587
AC:
89168
AN:
151962
Hom.:
27404
Cov.:
32
AF XY:
0.580
AC XY:
43065
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.762
Gnomad4 AMR
AF:
0.548
Gnomad4 ASJ
AF:
0.530
Gnomad4 EAS
AF:
0.436
Gnomad4 SAS
AF:
0.605
Gnomad4 FIN
AF:
0.392
Gnomad4 NFE
AF:
0.533
Gnomad4 OTH
AF:
0.559
Alfa
AF:
0.543
Hom.:
47471
Bravo
AF:
0.605
Asia WGS
AF:
0.547
AC:
1904
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
0.29
DANN
Benign
0.50

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: rs4924; hg19: chr16-56396486; COSMIC: COSV51923832; COSMIC: COSV51923832; API