chr16-56362574-C-T

Position:

• chr16-56362574-C-T

Variant summary

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

The ENST00000290649.10(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 ENST00000290649.10 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

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=-0.86).
• 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/exons	MANE	Protein	UniProt
AMFR	NM_001144.6	c.*335G>A		3_prime_UTR_variant	14/14	ENST00000290649.10	NP_001135.3
AMFR	NM_001323511.2	c.*335G>A		3_prime_UTR_variant	14/14		NP_001310440.1
AMFR	NM_001323512.2	c.*335G>A		3_prime_UTR_variant	15/15		NP_001310441.1
AMFR	XM_005255890.5	c.*335G>A		3_prime_UTR_variant	14/14		XP_005255947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AMFR	ENST00000290649.10	c.*335G>A		3_prime_UTR_variant	14/14	1	NM_001144.6	ENSP00000290649	P1
AMFR	ENST00000492830.5	c.*335G>A		3_prime_UTR_variant	7/7	2		ENSP00000473636
AMFR	ENST00000566757.1	n.1272G>A		non_coding_transcript_exon_variant	1/1
AMFR	ENST00000568325.1	n.679G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89100 AN: 151844 Hom.: 27378 Cov.: 32

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

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

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

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

Other links and lift over

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