rs2440468

Positions:

• chr16-56386682-G-A
• chr16-56386682-G-C

Variant summary

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

The NM_001144.6(AMFR):​c.1277-660C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,078 control chromosomes in the GnomAD database, including 27,295 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 (27295 hom., cov: 33)
• Consequence: AMFR NM_001144.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AMFR	NM_001144.6	c.1277-660C>T		intron_variant		ENST00000290649.10	NP_001135.3
AMFR	NM_001323511.2	c.992-660C>T		intron_variant			NP_001310440.1
AMFR	NM_001323512.2	c.1373-660C>T		intron_variant			NP_001310441.1
AMFR	XM_005255890.5	c.992-660C>T		intron_variant			XP_005255947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMFR	ENST00000290649.10	c.1277-660C>T		intron_variant		1	NM_001144.6	ENSP00000290649	P1
AMFR	ENST00000492830.5	c.245-660C>T		intron_variant		2		ENSP00000473636
AMFR	ENST00000567738.1	c.518-660C>T		intron_variant		5		ENSP00000456288
AMFR	ENST00000568762.1	n.44-660C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89020 AN: 151960 Hom.: 27269 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.586 AC: 89086 AN: 152078 Hom.: 27295 Cov.: 33 AF XY: 0.579 AC XY: 43040 AN XY: 74312

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.559

Alfa AF: 0.526 Hom.: 8547

Bravo AF: 0.604

Asia WGS AF: 0.546 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.084
DANN	Benign	0.39

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: rs2440468; hg19: chr16-56420594;