rs2432540

chr16-56385716-G-A

Variant summary

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

The NM_001144.6(AMFR):c.1380+203C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 572,058 control chromosomes in the GnomAD database, including 90,516 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 0.60 (28272 hom., cov: 30)
  • Exomes 𝑓: 0.54 (62244 hom.)
• Consequence: AMFR NM_001144.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AMFR	NM_001144.6	c.1380+203C>T		intron_variant		ENST00000290649.10
AMFR	NM_001323511.2	c.1095+203C>T		intron_variant
AMFR	NM_001323512.2	c.1476+203C>T		intron_variant
AMFR	XM_005255890.5	c.1095+203C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AMFR	ENST00000290649.10	c.1380+203C>T		intron_variant		1	NM_001144.6	P1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90207 AN: 151484 Hom.: 28237 Cov.: 30

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.572

GnomAD4 exome AF: 0.539 AC: 226624 AN: 420456 Hom.: 62244 Cov.: 4 AF XY: 0.544 AC XY: 120224 AN XY: 221126

Gnomad4 AFR exome AF: 0.784

Gnomad4 AMR exome AF: 0.556

Gnomad4 ASJ exome AF: 0.530

Gnomad4 EAS exome AF: 0.495

Gnomad4 SAS exome AF: 0.612

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.534

Gnomad4 OTH exome AF: 0.545

GnomAD4 genome AF: 0.596 AC: 90287 AN: 151602 Hom.: 28272 Cov.: 30 AF XY: 0.589 AC XY: 43596 AN XY: 73976

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.568

Alfa AF: 0.580 Hom.: 5023

Bravo AF: 0.614

Asia WGS AF: 0.550 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	4.3
Dann	Benign	0.82

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: rs2432540; hg19: chr16-56419628;