rs2550303

Positions:

• chr16-56361698-G-A
• chr16-56361698-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144.6(AMFR):​c.*1211C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 147,420 control chromosomes in the GnomAD database, including 33,375 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 0.66 (33338 hom., cov: 24)
  • Exomes 𝑓: 0.45 (37 hom.)
• Consequence: AMFR NM_001144.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMFR	NM_001144.6	c.*1211C>T		3_prime_UTR_variant	14/14	ENST00000290649.10	NP_001135.3
AMFR	NM_001323512.2	c.*1211C>T		3_prime_UTR_variant	15/15		NP_001310441.1
AMFR	NM_001323511.2	c.*1211C>T		3_prime_UTR_variant	14/14		NP_001310440.1
AMFR	XM_005255890.5	c.*1211C>T		3_prime_UTR_variant	14/14		XP_005255947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMFR	ENST00000290649	c.*1211C>T		3_prime_UTR_variant	14/14	1	NM_001144.6	ENSP00000290649.5
AMFR	ENST00000492830	c.*1211C>T		3_prime_UTR_variant	7/7	2		ENSP00000473636.1

Frequencies

GnomAD3 genomes AF: 0.661 AC: 97050 AN: 146900 Hom.: 33297 Cov.: 24

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.526

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 0.451 AC: 194 AN: 430 Hom.: 37 Cov.: 0 AF XY: 0.465 AC XY: 120 AN XY: 258

Gnomad4 FIN exome AF: 0.445

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.661 AC: 97131 AN: 146990 Hom.: 33338 Cov.: 24 AF XY: 0.659 AC XY: 46843 AN XY: 71042

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.634

Alfa AF: 0.611 Hom.: 10318

Bravo AF: 0.671

Asia WGS AF: 0.707 AC: 2454 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	7.1
DANN	Benign	0.52
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs2550303; hg19: chr16-56395610; COSMIC: COSV51920931; COSMIC: COSV51920931;